# Code Ocean User Guide

## v2.5.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.5.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.5.0/compute-capsule-basics/version-control.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.5.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.5.0/sharing-draft.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.5.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.5.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.5.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.5.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.5.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.5.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.5.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.5.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Dataset](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.5.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.5.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.5.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.5.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Datasets](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/components-of-a-pipeline/datasets.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/components-of-a-pipeline/map-paths.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.5.0/pipeline-guide/advanced-details-technical-structure.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.5.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.5.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.5.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.5.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.5.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.5.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.5.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.5.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.5.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.5.0/how-to.md)
- [How to use Git credentials during docker build](https://docs.codeocean.com/user-guide/v2.5.0/how-to/how-to-use-git-credentials-during-docker-build.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.5.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.5.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.5.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.5.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.5.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.5.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.5.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.5.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.5.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.5.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.5.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.5.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.5.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.5.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.5.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.5.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.5.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.5.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.5.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.5.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.5.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.5.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.5.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.5.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.5.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.5.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.5.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.5.0/support-and-troubleshooting.md)

## v2.6.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.6.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.6.0/compute-capsule-basics/version-control.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.6.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.6.0/sharing-draft.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.6.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.6.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.6.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.6.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.6.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.6.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.6.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.6.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Dataset](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.6.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.6.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.6.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.6.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.6.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Datasets](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/components-of-a-pipeline/datasets.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/components-of-a-pipeline/map-paths.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/advanced-details-technical-structure.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.6.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.6.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.6.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.6.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.6.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.6.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.6.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.6.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.6.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.6.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.6.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.6.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.6.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.6.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.6.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.6.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.6.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.6.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.6.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.6.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.6.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.6.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.6.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.6.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.6.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.6.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.6.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.6.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.6.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.6.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.6.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.6.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.6.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.6.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.6.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.6.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.6.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.6.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.6.0/support-and-troubleshooting.md)

## v2.7.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.7.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.7.0/compute-capsule-basics/version-control.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.7.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.7.0/sharing-draft.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.7.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.7.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.7.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.7.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.7.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.7.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.7.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.7.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Dataset](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.7.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.7.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.7.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.7.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.7.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Datasets](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/components-of-a-pipeline/datasets.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/components-of-a-pipeline/map-paths.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/advanced-details-technical-structure.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.7.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.7.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.7.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.7.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.7.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.7.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.7.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.7.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.7.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.7.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.7.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.7.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.7.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.7.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.7.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.7.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.7.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.7.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.7.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.7.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.7.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.7.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.7.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.7.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.7.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.7.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.7.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.7.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.7.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.7.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.7.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.7.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.7.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.7.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.7.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.7.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.7.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.7.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.7.0/support-and-troubleshooting.md)

## v2.8.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.8.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.8.0/compute-capsule-basics/version-control.md)
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.8.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.8.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.8.0/sharing-draft.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.8.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.8.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.8.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.8.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.8.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.8.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.8.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.8.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.8.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.8.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.8.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.8.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.8.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Datasets](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/components-of-a-pipeline/datasets.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/components-of-a-pipeline/map-paths.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/advanced-details-technical-structure.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.8.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.8.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.8.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.8.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.8.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.8.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.8.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.8.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.8.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.8.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.8.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.8.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.8.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.8.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.8.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.8.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.8.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.8.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.8.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.8.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.8.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.8.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.8.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.8.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.8.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.8.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.8.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.8.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.8.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.8.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.8.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.8.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.8.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.8.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.8.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.8.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.8.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.8.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.8.0/support-and-troubleshooting.md)

## v2.9.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.9.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.9.0/compute-capsule-basics/version-control.md)
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.9.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.9.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.9.0/sharing-draft.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.9.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.9.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.9.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.9.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.9.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.9.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.9.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.9.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.9.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.9.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.9.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.9.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.9.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Datasets](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/components-of-a-pipeline/datasets.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/components-of-a-pipeline/map-paths.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/advanced-details-technical-structure.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.9.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.9.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.9.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.9.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.9.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.9.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.9.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.9.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.9.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.9.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.9.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.9.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.9.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.9.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.9.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.9.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.9.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.9.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.9.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.9.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.9.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.9.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.9.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.9.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.9.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.9.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.9.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.9.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.9.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.9.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.9.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.9.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.9.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.9.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.9.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.9.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.9.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.9.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.9.0/support-and-troubleshooting.md)

## v2.10.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.10.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/cloud-workstation/running-rshiny-in-code-ocean.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/version-control.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.10.0/compute-capsule-basics/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity.
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.10.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.10.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.10.0/sharing-draft.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.10.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.10.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.10.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.10.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.10.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.10.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.10.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.10.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Tracking Result with Lineage Graph](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result/tracking-result-with-lineage-graph.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.10.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.10.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.10.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.10.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.10.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Git Sync for GitHub Integration](https://docs.codeocean.com/user-guide/v2.10.0/git-provider-integration-guide/git-sync-for-github-integration.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Datasets](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/components-of-a-pipeline/datasets.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/components-of-a-pipeline/map-paths.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/advanced-details-technical-structure.md)
- [Released Pipeline](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/released-pipeline.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.10.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.10.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.10.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.10.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.10.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.10.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.10.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.10.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.10.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.10.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.10.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.10.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.10.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.10.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.10.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.10.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.10.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.10.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.10.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.10.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.10.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.10.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.10.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.10.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.10.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.10.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.10.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.10.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.10.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.10.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.10.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.10.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.10.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.10.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.10.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.10.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.10.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.10.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.10.0/support-and-troubleshooting.md)

## v2.11.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.11.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/cloud-workstation/running-rshiny-in-code-ocean.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/version-control.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.11.0/compute-capsule-basics/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity.
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.11.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.11.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.11.0/sharing-capsule.md)
- [Released Capsules](https://docs.codeocean.com/user-guide/v2.11.0/publishing.md): This guide introduces Released Capsules and Internal Releases, as well as how to create and use a Released Capsule.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.11.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.11.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.11.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.11.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.11.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Creator Guide](https://docs.codeocean.com/user-guide/v2.11.0/app-panel-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [Viewer Guide](https://docs.codeocean.com/user-guide/v2.11.0/app-panel-guide/viewer-guide.md): Learn to use an existing App Panel in the Code Ocean IDE.
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.11.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.11.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.11.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.11.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.11.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Git Sync for GitHub Integration](https://docs.codeocean.com/user-guide/v2.11.0/git-provider-integration-guide/git-sync-for-github-integration.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Data](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline/data.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from data asset to capsule and between capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the pipeline runs.
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/advanced-details-technical-structure.md)
- [Released Pipeline](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/released-pipeline.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.11.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.11.0/code-ocean-api.md): Enables customers to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.11.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.11.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.11.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.11.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.11.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.11.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.11.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.11.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.11.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.11.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.11.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.11.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.11.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.11.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.11.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.11.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.11.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.11.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.11.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.11.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.11.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.11.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.11.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.11.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.11.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.11.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.11.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.11.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.11.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.11.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.11.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.11.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.11.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.11.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.11.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.11.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.11.0/support-and-troubleshooting.md)

## v2.12.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.12.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Fixing Environment building issues with buildlog](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/fixing-environment-building-issues-with-buildlog.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/cloud-workstation/running-streamlit-in-code-ocean.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/version-control.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.12.0/compute-capsule-basics/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity.
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.12.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.12.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.12.0/sharing-capsule.md)
- [Release Capsules](https://docs.codeocean.com/user-guide/v2.12.0/publishing.md): This guide introduces Release Capsules and Internal Releases, and how to create and use Release Capsules.
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.12.0/publishing/creating-and-using-release-capsules.md)
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.12.0/publishing/internal-releases.md)
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.12.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.12.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.12.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.12.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-apps.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Builder Guide](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide.md)
- [App Builder Tutorial](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [1. Prepare a New Capsule with Sample Files](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide/creator-guide/1.-prepare-a-new-capsule-with-sample-files.md)
- [2. Create a user interface in the App Builder](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide/creator-guide/2.-create-a-user-interface-in-the-app-builder.md)
- [3. Release The capsule with App panel (optional)](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide/creator-guide/3.-release-the-capsule-with-app-panel-optional.md)
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide/app-builder-user-interface.md)
- [Release App Panel Capsule](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/builder-guide/release-app-panel-capsule.md)
- [Run Guide](https://docs.codeocean.com/user-guide/v2.12.0/app-panel-guide/viewer-guide.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/creating-a-new-data-asset/custom-metadata.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/searching-a-data-asset.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.12.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.12.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.12.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.12.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.12.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Git Sync for GitHub Integration](https://docs.codeocean.com/user-guide/v2.12.0/git-provider-integration-guide/git-sync-for-github-integration.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Data](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline/data.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from data asset to capsule and between capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the pipeline runs.
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/advanced-details-technical-structure.md)
- [Released Pipeline](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/released-pipeline.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.12.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-api/data-asset-api.md)
- [Swagger Documentation](https://docs.codeocean.com/user-guide/v2.12.0/code-ocean-api/swagger-documentation.md): Public API Swagger Documentation
- [FAQ](https://docs.codeocean.com/user-guide/v2.12.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.12.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.12.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.12.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.12.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.12.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.12.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.12.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.12.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.12.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.12.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.12.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.12.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.12.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.12.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.12.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.12.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.12.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.12.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.12.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.12.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.12.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.12.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.12.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.12.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.12.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.12.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.12.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.12.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.12.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.12.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.12.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.12.0/support-and-troubleshooting.md)

## v2.13.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.13.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Fixing Environment building issues with buildlog](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/fixing-environment-building-issues-with-buildlog.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/cloud-workstation/running-streamlit-in-code-ocean.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/version-control.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.13.0/compute-capsule-basics/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity.
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.13.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.13.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.13.0/sharing-capsule.md)
- [Release Capsules](https://docs.codeocean.com/user-guide/v2.13.0/publishing.md): This guide introduces Release Capsules and Internal Releases, and how to create and use Release Capsules.
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.13.0/publishing/creating-and-using-release-capsules.md)
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.13.0/publishing/internal-releases.md)
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.13.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.13.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.13.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.13.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-apps/quality-control.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Builder Guide](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide.md)
- [App Builder Tutorial](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [1. Prepare a New Capsule with Sample Files](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide/creator-guide/1.-prepare-a-new-capsule-with-sample-files.md)
- [2. Create a user interface in the App Builder](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide/creator-guide/2.-create-a-user-interface-in-the-app-builder.md)
- [3. Release The capsule with App panel (optional)](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide/creator-guide/3.-release-the-capsule-with-app-panel-optional.md)
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide/app-builder-user-interface.md)
- [Release App Panel Capsule](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/builder-guide/release-app-panel-capsule.md)
- [Run Guide](https://docs.codeocean.com/user-guide/v2.13.0/app-panel-guide/viewer-guide.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/creating-a-new-data-asset/custom-metadata.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/searching-a-data-asset.md)
- [Discovering Data Assets](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/discovering-data-assets.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.13.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.13.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.13.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.13.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.13.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Git Sync for GitHub Integration](https://docs.codeocean.com/user-guide/v2.13.0/git-provider-integration-guide/git-sync-for-github-integration.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Data](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline/data.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from data asset to capsule and between capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the pipeline runs.
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/advanced-details-technical-structure.md)
- [Released Pipeline](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/released-pipeline.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.13.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-api/data-asset-api.md)
- [Swagger Documentation](https://docs.codeocean.com/user-guide/v2.13.0/code-ocean-api/swagger-documentation.md): Public API Swagger Documentation
- [FAQ](https://docs.codeocean.com/user-guide/v2.13.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.13.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.13.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.13.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.13.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.13.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.13.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.13.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.13.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.13.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.13.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.13.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.13.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.13.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.13.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.13.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.13.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.13.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.13.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.13.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.13.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.13.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.13.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.13.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.13.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.13.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.13.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.13.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.13.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.13.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.13.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.13.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.13.0/support-and-troubleshooting.md)

## v2.14.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.14.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Code](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Fixing Environment building issues with buildlog](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/fixing-environment-building-issues-with-buildlog.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/cloud-workstation/running-streamlit-in-code-ocean.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/version-control.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.14.0/compute-capsule-basics/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity.
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.14.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.14.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.14.0/sharing-capsule.md)
- [Release Capsules](https://docs.codeocean.com/user-guide/v2.14.0/publishing.md): This guide introduces Release Capsules and Internal Releases, and how to create and use Release Capsules.
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.14.0/publishing/creating-and-using-release-capsules.md)
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.14.0/publishing/internal-releases.md)
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.14.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.14.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.14.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.14.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-apps/quality-control.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Builder Guide](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide.md)
- [App Builder Tutorial](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [1. Prepare a New Capsule with Sample Files](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide/creator-guide/1.-prepare-a-new-capsule-with-sample-files.md)
- [2. Create a user interface in the App Builder](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide/creator-guide/2.-create-a-user-interface-in-the-app-builder.md)
- [3. Release The capsule with App panel (optional)](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide/creator-guide/3.-release-the-capsule-with-app-panel-optional.md)
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide/app-builder-user-interface.md)
- [Release App Panel Capsule](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/builder-guide/release-app-panel-capsule.md)
- [Run Guide](https://docs.codeocean.com/user-guide/v2.14.0/app-panel-guide/viewer-guide.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/creating-a-new-data-asset/custom-metadata.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/searching-a-data-asset.md)
- [Discovering Data Assets](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/discovering-data-assets.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.14.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.14.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.14.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.14.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials during Capsule Build](https://docs.codeocean.com/user-guide/v2.14.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Git Sync for GitHub Integration](https://docs.codeocean.com/user-guide/v2.14.0/git-provider-integration-guide/git-sync-for-github-integration.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/create-a-pipeline-in-5-minutes.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Data](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline/data.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from data asset to capsule and between capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the pipeline runs.
- [Bash Scripting for Pipeline Capsules](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/bash-scripting-for-pipeline-capsules.md)
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/advanced-details-technical-structure.md)
- [Released Pipeline](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/released-pipeline.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.14.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-api/data-asset-api.md)
- [Swagger Documentation](https://docs.codeocean.com/user-guide/v2.14.0/code-ocean-api/swagger-documentation.md): Public API Swagger Documentation
- [FAQ](https://docs.codeocean.com/user-guide/v2.14.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.14.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.14.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.14.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.14.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.14.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.14.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.14.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.14.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.14.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.14.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.14.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.14.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.14.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.14.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.14.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.14.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.14.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.14.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.14.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.14.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.14.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.14.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.14.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.14.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.14.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.14.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.14.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.14.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.14.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.14.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.14.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.14.0/support-and-troubleshooting.md)

## v2.15.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/master.md)
- [How to create a capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.15.0/how-to-create-a-capsule-in-5-minutes.md)
- [Compute Capsule Guide](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics.md): Learn all the basic concepts of a compute capsule—the fundamental unit of a research project in Code Ocean
- [The Structure of a Compute Capsule](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Environment Editor](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-environment-editor.md)
- [Select a Starter Environment](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/starter-environment.md)
- [Setting Up New or Additional Languages](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/setting-up-new-or-additional-languages.md)
- [MATLAB: Additional Settings](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/additional-setting-for-matlab.md)
- [Dockerfile](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-docker-file.md)
- [Packages and Package Managers](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/packages-and-package-manager.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Using the Post-Install Script](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/environment/compute-resources.md)
- [Code](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Running a Capsule with Reproducible Run](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/running-a-capsule-with-reproducible-run.md)
- [Fixing Environment building issues with buildlog](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/fixing-environment-building-issues-with-buildlog.md)
- [Working From a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation/launching-a-cloud-workstation.md)
- [Using Code Ocean Tools in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation/using-code-ocean-tools-in-a-cloud-workstation.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Cloud Workstation Computational Process Window](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation/cloud-workstation-computational-process-window.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/cloud-workstation/running-streamlit-in-code-ocean.md)
- [Version Control](https://docs.codeocean.com/user-guide/v2.15.0/compute-capsule-basics/version-control.md)
- [Adding VSCode Extensions to your Code Ocean Capsule Environment](https://docs.codeocean.com/user-guide/v2.15.0/adding-vscode-extensions-to-your-code-ocean-capsule-environment.md)
- [Archive Capsule/Dataset](https://docs.codeocean.com/user-guide/v2.15.0/archive-capsule-dataset.md): Capsules and data assets can be archived to reduce clutter in the capsules/data assets list. Archiving removes a capsule/data asset from the 'All' view, making them accessible through the Archive view
- [Sharing Compute Capsules](https://docs.codeocean.com/user-guide/v2.15.0/sharing-capsule.md)
- [Release Capsules](https://docs.codeocean.com/user-guide/v2.15.0/publishing.md): This guide introduces Release Capsules and Internal Releases, and how to create and use Release Capsules.
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.15.0/publishing/creating-and-using-release-capsules.md)
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.15.0/publishing/internal-releases.md)
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.15.0/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.15.0/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.15.0/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.15.0/secret-management-guide/collaborating-a-capsule-with-secret.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/use-cases-and-examples.md): These are real world examples of how to use Apps Library capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): How to use the Data Connector capsules using Snowflake as an example
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the GSEA App
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide.md): Learn to create and use App Panel in the compute capsule IDE
- [Builder Guide](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide.md)
- [App Builder Tutorial](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide/creator-guide.md): Learn to create an App Panel with sample files step-by-step. It takes ~10min to complete
- [1. Prepare a New Capsule with Sample Files](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide/creator-guide/1.-prepare-a-new-capsule-with-sample-files.md)
- [2. Create a user interface in the App Builder](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide/creator-guide/2.-create-a-user-interface-in-the-app-builder.md)
- [3. Release The capsule with App panel (optional)](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide/creator-guide/3.-release-the-capsule-with-app-panel-optional.md)
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide/app-builder-user-interface.md)
- [Release App Panel Capsule](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/builder-guide/release-app-panel-capsule.md)
- [Run Guide](https://docs.codeocean.com/user-guide/v2.15.0/app-panel-guide/viewer-guide.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide.md): Learn to create, use and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/creating-a-new-data-asset.md)
- [Adding a New Data Asset](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/creating-a-new-data-asset/adding-a-new-dataset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/creating-a-new-data-asset/custom-metadata.md)
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/creating-a-new-data-asset/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Working with Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/searching-a-data-asset.md)
- [Discovering Data Assets](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/discovering-data-assets.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.15.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.15.0/git-provider-integration-guide.md): Learn to sync a compute capsule with a repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.15.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Creating a New Capsule by Cloning a Git Repository](https://docs.codeocean.com/user-guide/v2.15.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Use Git Credentials During Capsule Build](https://docs.codeocean.com/user-guide/v2.15.0/git-provider-integration-guide/use-git-credentials-during-capsule-build.md): Clone a private Git repository in the postInstall script
- [Git Sync for Git Integration](https://docs.codeocean.com/user-guide/v2.15.0/git-provider-integration-guide/git-sync-for-git-integration.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide.md): This guide introduces the Code Ocean pipeline feature. The Getting started section covers how to create a pipeline in 5 minutes. Each component of the pipeline is explained separately.
- [Getting Started](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/getting-started.md)
- [Create a pipeline in 5 minutes (Update)](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/create-a-pipeline-in-5-minutes-update.md): This demonstration provides the steps for building a simple pipeline and processing data in parallel using Code Ocean Pipelines.
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline/capsules.md)
- [Data](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline/data.md)
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline/results-bucket.md)
- [Map Paths](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from data asset to capsule and between capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md)
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the pipeline runs.
- [Running Code in Parallel Using Pipelines](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/running-code-in-parallel-using-pipelines.md): Strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Troubleshooting Tips](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/troubleshooting-tips.md)
- [How-to-Guide: Bioinformatics Tools](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/how-to-guide-bioinformatics-tools.md)
- [Advanced Details (Technical Structure)](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/advanced-details-technical-structure.md)
- [Released Pipeline](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/released-pipeline.md)
- [FAQs](https://docs.codeocean.com/user-guide/v2.15.0/pipeline-guide/faqs.md)
- [Publishing from Code Ocean Private Cloud to Public Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/publishing-from-code-ocean-private-cloud-to-public-code-ocean.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Getting the Code Ocean API Tokens](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-api/getting-the-code-ocean-api-tokens.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-api/capsule-api.md)
- [Pipeline API](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-api/pipeline-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.15.0/code-ocean-api/data-asset-api.md)
- [FAQ](https://docs.codeocean.com/user-guide/v2.15.0/faq.md)
- [FAQ—General](https://docs.codeocean.com/user-guide/v2.15.0/faq/faq-general.md)
- [FAQ—Building Environment](https://docs.codeocean.com/user-guide/v2.15.0/faq/faq-building-environment.md)
- [FAQ—GitHub Integration](https://docs.codeocean.com/user-guide/v2.15.0/faq/github-integration.md)
- [How To](https://docs.codeocean.com/user-guide/v2.15.0/how-to.md)
- [Saving Files](https://docs.codeocean.com/user-guide/v2.15.0/how-to/saving-files.md)
- [Debugging and remedying installation issues for R packages on Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/how-to/debugging-and-remedying-installation-issues-for-r-packages-on-code-ocean.md)
- [Using matplotlib with no display attached](https://docs.codeocean.com/user-guide/v2.15.0/how-to/using-matplotlib-with-no-display-attached.md): Solving "RuntimeError: Invalid DISPLAY variable" in Python.
- [Installing user-provided MATLAB toolboxes](https://docs.codeocean.com/user-guide/v2.15.0/how-to/installing-user-provided-matlab-toolboxes.md): Downloading and installing CVX, VLFeat, MOSEK, YALMIP, etc. using postInstall functionality.
- [Installing Python 2 on Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/how-to/installing-python-2-on-code-ocean.md): Start from a python 3 environment and install python version 2
- [Installing R in a non-R environment, or updating to the most recent version](https://docs.codeocean.com/user-guide/v2.15.0/how-to/installing-r-in-a-non-r-environment-or-updating-to-the-most-recent-version.md): How to add a recent R version to any environment
- [How do I find a particular file in the environment](https://docs.codeocean.com/user-guide/v2.15.0/how-to/how-do-i-find-a-particular-file-in-the-environment.md): Use the Linux command "find"
- [Knitting an Rmarkdown document](https://docs.codeocean.com/user-guide/v2.15.0/how-to/knitting-an-rmarkdown-document.md): How to render Rmarkdown documents reproducibly and save the output to the results folder
- [Rendering Jupyter notebooks to HTML](https://docs.codeocean.com/user-guide/v2.15.0/how-to/rendering-jupyter-notebooks-to-html.md): How to execute notebooks reproducibly and save the output to the results folder
- [Converting a Jupyter notebook to the latest version](https://docs.codeocean.com/user-guide/v2.15.0/how-to/converting-a-jupyter-notebook-to-the-latest-version.md): Make your old notebook shiny and new again with one simple command
- [Use MRAN snapshots to install archived R packages](https://docs.codeocean.com/user-guide/v2.15.0/how-to/use-mran-snapshots-to-install-archived-r-packages.md): How to match your computational environment to the R packages available in a prior time
- [Install additional Jupyter kernels](https://docs.codeocean.com/user-guide/v2.15.0/how-to/install-additional-jupyter-kernels.md): Python, R, and Stata kernels on Code Ocean.
- [Uploading a Cover Image](https://docs.codeocean.com/user-guide/v2.15.0/how-to/uploading-a-cover-image.md): For discovery and intelligibility on Code Ocean's Internal Releases page
- [Duplicating a Compute Capsule](https://docs.codeocean.com/user-guide/v2.15.0/how-to/duplicating-a-compute-capsule.md): How to create a private copy of either released or unreleased code.
- [Should I delete \`sudo\` commands on Code Ocean?](https://docs.codeocean.com/user-guide/v2.15.0/how-to/should-i-delete-sudo-commands-on-code-ocean.md): Yes. You are the root user on your Code Ocean Capsule
- [Why code files modification times are not being preserved after re-launching a cloud workstation?](https://docs.codeocean.com/user-guide/v2.15.0/how-to/why-code-files-modification-times-are-not-being-preserved-after-re-launching-a-cloud-workstation.md)
- [How to save results to /results \*only if\* code is being executed on Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/how-to/how-to-save-results-to-results-only-if-code-is-being-executed-on-code-ocean.md): Using either Linux shell scripting or built-in MATLAB syntax.
- [Can I upload folders to Code Ocean?](https://docs.codeocean.com/user-guide/v2.15.0/how-to/can-i-upload-folders-to-code-ocean.md): Yes, but maybe not on Safari (use Chrome or Firefox to do so).
- [How can I upgrade built–in packages (e.g. pip)?](https://docs.codeocean.com/user-guide/v2.15.0/how-to/how-can-i-upgrade-built-in-packages-e.g.-pip.md)
- [What is a compute capsule?](https://docs.codeocean.com/user-guide/v2.15.0/how-to/what-is-a-compute-capsule.md): What is a compute capsule?
- [Exporting capsules and reproducing results on your local machine](https://docs.codeocean.com/user-guide/v2.15.0/how-to/exporting-capsules-and-reproducing-results-on-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Running code with GPU support](https://docs.codeocean.com/user-guide/v2.15.0/how-to/running-code-with-gpu-support.md): Select a base environment with GPU support
- [Adding a Code Ocean capsule as a remote to an existing git repository](https://docs.codeocean.com/user-guide/v2.15.0/how-to/adding-a-code-ocean-capsule-as-a-remote-to-an-existing-git-repository.md): For integrating Code Ocean into your local development process.
- [Installing R packages through postInstall](https://docs.codeocean.com/user-guide/v2.15.0/how-to/installing-r-packages-through-postinstall.md): A few notes on flags and parameters you may need to add
- [Git clone your capsule to your computer](https://docs.codeocean.com/user-guide/v2.15.0/how-to/git-clone-your-capsule-to-your-computer.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/how-to/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using capsule paths in my code](https://docs.codeocean.com/user-guide/v2.15.0/how-to/using-capsule-paths-in-my-code.md)
- [Monitoring and inspecting the result of the environment setup phase](https://docs.codeocean.com/user-guide/v2.15.0/how-to/monitoring-and-inspecting-the-result-of-the-environment-setup-phase.md)
- [What is apt-get?](https://docs.codeocean.com/user-guide/v2.15.0/how-to/what-is-apt-get.md): Installing Linux packages.
- [Setting up new or additional languages on Code Ocean via the package managers](https://docs.codeocean.com/user-guide/v2.15.0/how-to/setting-up-new-or-additional-languages-on-code-ocean-via-the-package-managers.md)
- [Compute Resources in Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/how-to/compute-resources-in-code-ocean.md): Code Ocean leverages AWS to provide you with access to any cloud computing resource that your Capsule requires. These resources fall under two categories: flex and dedicated machines.
- [Dockerfiles in Code Ocean](https://docs.codeocean.com/user-guide/v2.15.0/how-to/dockerfiles-in-code-ocean.md)
- [Support & Troubleshooting](https://docs.codeocean.com/user-guide/v2.15.0/support-and-troubleshooting.md)

## v2.16.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.16.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.16.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.16.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to Your Local Machine](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.16.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment/packages-and-package-manager.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.16.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.16.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.16.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/managing-pipelines.md)
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [The Nextflow folder](https://docs.codeocean.com/user-guide/v2.16.0/pipeline-guide/the-nextflow-folder.md)
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.16.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.16.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.16.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.16.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.16.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.16.0/app-panel-guide.md): App Panel provides insights from Capsules. It enables researchers to interact with Capsules without using the code. With key user-input parameters, you can use the App Panel to generate results.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.16.0/app-panel-guide/app-builder-user-interface.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.16.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.16.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.16.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.16.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.16.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.16.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Authentication](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-api/authentication.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.16.0/code-ocean-api/data-asset-api.md)
- [More Support](https://docs.codeocean.com/user-guide/v2.16.0/more-support.md)

## v2.17.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.17.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.17.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.17.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [App Builder](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel/app-builder.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your local machine](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.17.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment/packages-and-package-manager.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.17.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.17.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.17.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/managing-pipelines.md)
- [How to run code in parallel](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [The Nextflow folder](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/the-nextflow-folder.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v2.17.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing nf-core.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.17.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.17.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.17.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.17.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.17.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.17.0/app-panel-guide.md): App Panel provides insights from Capsules. It enables researchers to interact with Capsules without using the code. With key user-input parameters, you can use the App Panel to generate results.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.17.0/app-panel-guide/app-builder-user-interface.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.17.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.17.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.17.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.17.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.17.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.17.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Authentication](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-api/authentication.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.17.0/code-ocean-api/data-asset-api.md)
- [More Support](https://docs.codeocean.com/user-guide/v2.17.0/more-support.md)

## v2.18.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.18.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.18.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.18.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your local machine](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.18.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment/packages-and-package-manager.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.18.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.18.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.18.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/managing-pipelines.md)
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [The Nextflow Folder](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/the-nextflow-folder.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing nf-core pipelines.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v2.18.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.18.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.18.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.18.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.18.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.18.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.18.0/app-panel-guide.md): App Panel provides insights from Capsules. It enables researchers to interact with Capsules without using the code. With key user-input parameters, you can use the App Panel to generate results.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.18.0/app-panel-guide/app-builder-user-interface.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.18.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.18.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.18.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.18.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.18.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.18.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-api.md): Enables users to interact with Code Ocean without using the web application
- [Authentication](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-api/authentication.md)
- [Capsule API](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-api/capsule-api.md)
- [Computation API](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-api/computation-api.md)
- [Data Asset API](https://docs.codeocean.com/user-guide/v2.18.0/code-ocean-api/data-asset-api.md)
- [More Support](https://docs.codeocean.com/user-guide/v2.18.0/more-support.md)

## v2.19.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.19.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.19.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.19.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your local machine](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.19.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment/packages-and-package-manager.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.19.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.19.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.19.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/managing-pipelines.md)
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [The Nextflow Folder](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/the-nextflow-folder.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v2.19.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.19.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.19.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.19.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.19.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.19.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.19.0/app-panel-guide.md): App Panel provides insights from Capsules. It enables researchers to interact with Capsules without using the code. With key user-input parameters, you can use the App Panel to generate results.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.19.0/app-panel-guide/app-builder-user-interface.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.19.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.19.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.19.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.19.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.19.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.19.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v2.19.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v2.19.0/more-support.md)

## v2.20.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.20.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.20.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.20.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your local machine](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.20.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.20.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.20.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.20.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/managing-pipelines.md)
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [The Nextflow Folder](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/the-nextflow-folder.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v2.20.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.20.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.20.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.20.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.20.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.20.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.20.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.20.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v2.20.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.20.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.20.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.20.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.20.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.20.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.20.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v2.20.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v2.20.0/more-support.md)

## v2.21.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.21.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.21.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.21.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [Results](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.21.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.21.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.21.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.21.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v2.21.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.21.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.21.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.21.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.21.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.21.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.21.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.21.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v2.21.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.21.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.21.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.21.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.21.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.21.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.21.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v2.21.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v2.21.0/more-support.md)

## v2.22.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/master.md)
- [Quick Start Guide](https://docs.codeocean.com/user-guide/v2.22.0/quick-start-guide.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v2.22.0/quick-start-guide/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v2.22.0/quick-start-guide/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v2.22.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v2.22.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal on Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-on-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop on Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-on-code-ocean.md)
- [Using MATLAB on Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-on-code-ocean.md)
- [Using VSCode On Code Ocean](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-on-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v2.22.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v2.22.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including released Capsules, those with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v2.22.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v2.22.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v2.22.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v2.22.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v2.22.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v2.22.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v2.22.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v2.22.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v2.22.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v2.22.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.22.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v2.22.0/app-panel-guide/viewer-guide.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v2.22.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v2.22.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v2.22.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v2.22.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v2.22.0/more-support.md)

## v3.0.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.0.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.0.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.0.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.0.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.0.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.0.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.0.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.0.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VSCode in Code Ocean](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/launching-a-cloud-workstation/using-vscode-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.0.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.0.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.0.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.0.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.0.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.0.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.0.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.0.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.0.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.0.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.0.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.0.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.0.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.0.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.0.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.0.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.0.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.0.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.0.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.0.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.0.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, or from the Capsule or Pipeline Timeline.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.0.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.0.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.0.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.0.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.0.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.0.0/more-support.md)

## v3.1.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.1.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.1.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.1.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.1.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.1.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.1.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.1.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.1.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.1.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.1.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.1.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.1.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.1.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.1.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.1.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.1.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.1.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.1.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.1.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.1.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.1.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.1.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.1.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.1.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.1.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.1.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.1.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.1.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.1.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, or from the Capsule or Pipeline Timeline.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.1.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.1.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.1.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.1.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.1.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.1.0/more-support.md)

## v3.2.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.2.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.2.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.2.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.2.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.2.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.2.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.2.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.2.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.2.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.2.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.2.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.2.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.2.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.2.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.2.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.2.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.2.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.2.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.2.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.2.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.2.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.2.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.2.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.2.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.2.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.2.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.2.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.2.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.2.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, or from the Capsule or Pipeline Timeline.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.2.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.2.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.2.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.2.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.2.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.2.0/more-support.md)

## v3.3.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.3.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.3.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.3.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.3.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.3.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.3.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.3.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.3.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.3.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.3.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.3.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.3.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.3.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.3.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.3.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.3.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.3.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.3.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.3.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.3.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.3.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.3.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.3.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.3.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.3.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.3.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.3.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.3.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.3.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, or from the Capsule or Pipeline Timeline.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.3.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.3.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.3.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.3.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.3.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.3.0/more-support.md)

## v3.4.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.4.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.4.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.4.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.4.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.4.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.4.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.4.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.4.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.4.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.4.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.4.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.4.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.4.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.4.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.4.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.4.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.4.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.4.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.4.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.4.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.4.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.4.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.4.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.4.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.4.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.4.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.4.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.4.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.4.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.4.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.4.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.4.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.4.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.4.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.4.0/more-support.md)

## v3.5.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.5.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.5.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.5.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.5.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.5.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.5.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.5.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.5.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.5.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.5.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.5.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.5.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.5.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.5.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.5.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.5.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.5.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.5.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.5.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.5.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.5.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.5.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.5.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.5.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.5.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.5.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.5.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.5.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.5.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.5.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.5.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.5.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.5.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.5.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.5.0/more-support.md)

## v3.6.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.6.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.6.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.6.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.6.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.6.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.6.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.6.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.6.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.6.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.6.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/managing-pipelines.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.6.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.6.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.6.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.6.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.6.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.6.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.6.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.6.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.6.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.6.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.6.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.6.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.6.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.6.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.6.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.6.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.6.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.6.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.6.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.6.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.6.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.6.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.6.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.6.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.6.0/more-support.md)

## v3.7.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.7.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.7.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.7.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.7.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.7.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.7.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.7.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.7.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.7.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.7.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.7.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.7.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.7.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md)
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.7.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.7.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.7.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.7.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.7.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.7.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.7.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.7.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.7.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.7.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.7.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.7.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.7.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.7.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.7.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.7.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.7.0/models-guide/managing-models.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.7.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.7.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.7.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.7.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.7.0/more-support.md)

## v3.8.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.8.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.8.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.8.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.8.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.8.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.8.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.8.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.8.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.8.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.8.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Timeline](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/the-pipeline-ui/timeline.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.8.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.8.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.8.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.8.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.8.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.8.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.8.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.8.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.8.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.8.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.8.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.8.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.8.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.8.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.8.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.8.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.8.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.8.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.8.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.8.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v3.8.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.8.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.8.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.8.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.8.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.8.0/more-support.md)

## v3.9.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v3.9.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v3.9.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v3.9.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v3.9.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v3.9.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v3.9.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v3.9.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v3.9.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v3.9.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v3.9.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v3.9.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v3.9.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v3.9.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v3.9.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v3.9.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v3.9.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v3.9.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v3.9.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v3.9.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v3.9.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.9.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v3.9.0/app-panel-guide/viewer-guide.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v3.9.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v3.9.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v3.9.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.9.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v3.9.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v3.9.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v3.9.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v3.9.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v3.9.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v3.9.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v3.9.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v3.9.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v3.9.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v3.9.0/more-support.md)

## v4.0.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.0.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.0.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.0.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.0.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.0.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.0.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.0.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.0.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.0.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.0.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.0.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.0.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.0.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.0.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.0.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.0.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.0.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.0.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.0.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.0.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.0.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.0.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.0.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.0.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.0.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.0.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.0.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.0.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.0.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.0.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.0.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.0.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.0.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.0.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.0.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.0.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.0.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.0.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.0.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.0.0/more-support.md)

## v4.1.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.1.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.1.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.1.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.1.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.1.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.1.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.1.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.1.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.1.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.1.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.1.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.1.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.1.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.1.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.1.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.1.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.1.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.1.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.1.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.1.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.1.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.1.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.1.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.1.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.1.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.1.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.1.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.1.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.1.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.1.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.1.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.1.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.1.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.1.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.1.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.1.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.1.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.1.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.1.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.1.0/more-support.md)

## v4.2.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.2.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.2.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.2.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.2.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.2.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.2.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.2.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.2.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.2.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.2.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.2.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.2.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.2.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.2.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.2.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.2.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.2.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.2.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.2.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.2.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.2.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.2.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.2.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.2.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.2.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.2.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.2.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.2.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.2.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.2.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.2.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.2.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.2.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.2.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.2.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.2.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.2.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.2.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.2.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.2.0/more-support.md)

## v4.3.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.3.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.3.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.3.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.3.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.3.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.3.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.3.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.3.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.3.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.3.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.3.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.3.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.3.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.3.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.3.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.3.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.3.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.3.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.3.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.3.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.3.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.3.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.3.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.3.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.3.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.3.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.3.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.3.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.3.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.3.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.3.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.3.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.3.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.3.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.3.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.3.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.3.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.3.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.3.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.3.0/more-support.md)

## v4.4.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.4.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.4.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.4.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.4.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.4.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.4.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.4.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.4.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.4.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.4.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.4.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.4.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.4.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.4.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.4.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.4.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.4.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.4.0/app-panel-guide/app-builder-user-interface.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.4.0/app-panel-guide/app-builder-user-interface/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.4.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.4.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.4.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.4.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.4.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.4.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.4.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.4.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.4.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.4.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.4.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.4.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.4.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.4.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.4.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.4.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.4.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.4.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.4.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.4.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.4.0/more-support.md)

## v4.5.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.5.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.5.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.5.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.5.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.5.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.5.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.5.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.5.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.5.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.5.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.5.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.5.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.5.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.5.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.5.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.5.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.5.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.5.0/app-panel-guide/creator-guide.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.5.0/app-panel-guide/creator-guide/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.5.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.5.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.5.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.5.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.5.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.5.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.5.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.5.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.5.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.5.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.5.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.5.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.5.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.5.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.5.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.5.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.5.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.5.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.5.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.5.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.5.0/more-support.md)

## v4.6.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/app-panel-guide/creator-guide.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/app-panel-guide/creator-guide/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/more-support.md)

## v4.7.0

- [Welcome to Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/master.md)
- [Onboarding](https://docs.codeocean.com/user-guide/v4.7.0/onboarding.md)
- [Quick Start Guides](https://docs.codeocean.com/user-guide/v4.7.0/onboarding/quick-start-guides.md): Start here to learn how to run a Capsule and use Capsules in Pipelines.
- [Create a Capsule in 5 minutes](https://docs.codeocean.com/user-guide/v4.7.0/onboarding/quick-start-guides/create-a-capsule-in-5-minutes.md): In Code Ocean, the unit used to create, organize, and share research projects is a Capsule. The Capsule contains the code, environment, data, and results of a run.
- [Create a Pipeline in 5 minutes](https://docs.codeocean.com/user-guide/v4.7.0/onboarding/quick-start-guides/create-a-pipeline-in-5-minutes.md): Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules.
- [Video Library](https://docs.codeocean.com/user-guide/v4.7.0/onboarding/video-library.md): A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
- [Key Concepts](https://docs.codeocean.com/user-guide/v4.7.0/key-concepts.md): An introduction to all key Code Ocean concepts and definitions in one page with links to further documentation.
- [Capsule Guide](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics.md): Learn all the basic concepts of a Capsule—the fundamental unit of a research project in Code Ocean.
- [The Capsule Interface](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/the-capsule-interface.md)
- [File Navigation/App Builder Panel](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/the-capsule-interface/file-navigation-app-builder-panel.md)
- [Editor Panel](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/the-capsule-interface/editor-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/the-capsule-interface/reproducibility-panel.md)
- [The Structure of a Capsule](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule.md)
- [Metadata](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/metadata.md)
- [Environment](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/environment.md)
- [Code](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/code.md)
- [Data](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/data.md)
- [.codeocean](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/.codeocean.md)
- [Scratch](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/scratch.md): Working with Intermediate Data in Code Ocean
- [Results](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/results.md)
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/structure-of-a-compute-capsule/capsule-settings.md)
- [Reproducible Runs](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/reproducible-runs.md): In order to perform a Reproducible Run from the Capsule IDE, the environment must be built and the run file must specify which script the Capsule should run.
- [Version Control](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/version-control.md)
- [Importing a Capsule from a Git Provider](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/version-control/importing-a-capsule-from-a-git-provider.md): Create a new Capsule by copying an existing git repository with a URL.
- [Clone via Git...](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/version-control/clone-via-git....md): Securely clone your pipeline’s Git repository so you can work locally or in another Git-enabled environment.
- [Managing Capsules](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/managing-capsules.md)
- [Sharing a Capsule with Secrets](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/managing-capsules/collaborating-a-capsule-with-secret.md)
- [Exporting Capsules to your Local Machine](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/managing-capsules/exporting-capsules-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Secret Management Guide](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/secret-management-guide.md): Learn how to manage and store your secrets and credentials to different systems in Code Ocean
- [Setting a Secret in the Account Settings Page](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/secret-management-guide/adding-editing-a-secret-in-the-account-settings-page.md)
- [Accessing a Secret in a Capsule](https://docs.codeocean.com/user-guide/v4.7.0/compute-capsule-basics/secret-management-guide/attaching-a-secret-to-a-capsule.md)
- [Setting up the Environment](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment.md)
- [Selecting a Starter Environment](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/starter-environment.md)
- [Package Managers and Adding Packages](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/packages-and-package-manager.md)
- [Installing R packages](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/installing-r-packages.md)
- [Environment Variables](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/environment-variables.md): Code Ocean specific environment variables are available during Reproducible Runs and Cloud Workstation Sessions to reduce coding complexity. Users can also create their own environment variables.
- [Build Log](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/build-log.md)
- [Post-Install Script](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/the-post-install-script.md)
- [Compute Resources](https://docs.codeocean.com/user-guide/v4.7.0/setting-up-the-environment/compute-resources.md)
- [Working in a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation.md)
- [Launching a Cloud Workstation](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation.md)
- [Running RShiny in Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation/running-rshiny-in-code-ocean.md)
- [Running Streamlit in Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation/running-streamlit-in-code-ocean.md)
- [Using Terminal in Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation/using-terminal-in-code-ocean.md): How to launch Terminal in the browser using Cloud Workstations.
- [Using Ubuntu Desktop in Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation/using-ubuntu-desktop-in-code-ocean.md)
- [Using MATLAB in Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation/using-matlab-in-code-ocean.md)
- [Using VS Code in Code Ocean](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/launching-a-cloud-workstation/using-vs-code-in-code-ocean.md)
- [Exiting a Cloud Workstation Session](https://docs.codeocean.com/user-guide/v4.7.0/cloud-workstation/types-of-terminating-a-cloud-workstation.md)
- [Data Assets Guide](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide.md): Learn to create, use, and share Data Assets in Code Ocean
- [Types of Data Assets](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/types-of-data-assets.md)
- [Creating a New Data Asset](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/adding-a-new-dataset.md): The process of creating new Data Assets is different depending upon the type of Data Asset being created.
- [Capturing a Result](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/capturing-a-result.md)
- [Provenance of the Result Data Asset](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/capturing-a-result/provenance-of-the-result-data-asset.md)
- [Using Data Assets in a Capsule](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/attaching-datasets-to-a-capsule.md)
- [Managing Data Assets](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/viewing-and-editing-data-assets.md)
- [Finding Data Assets](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/viewing-and-editing-data-assets/searching-a-data-asset.md)
- [Custom Metadata](https://docs.codeocean.com/user-guide/v4.7.0/data-assets-guide/viewing-and-editing-data-assets/custom-metadata.md)
- [Pipeline Guide](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide.md)
- [The Pipeline UI](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/the-pipeline-ui.md)
- [File Tree System](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/the-pipeline-ui/file-tree-system.md)
- [Pipeline App Panel](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/the-pipeline-ui/pipeline-app-panel.md)
- [Reproducibility Panel](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/the-pipeline-ui/reproducibility-panel.md)
- [Components of a Pipeline](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline.md)
- [Nextflow File](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/nextflow-file.md)
- [Capsules](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/capsules.md): This sections explains how to use a Capsule in a Pipeline, including release Capsules, Capsules with secrets, changing Capsule resources, and removing or replacing Capsules.
- [Data](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/data.md): This section explains how to use data in a Pipeline, including external Data Assets, and how to remove or replace data.
- [Results Bucket](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/results-bucket.md): This section explains how to save and view the output of a Pipeline.
- [Map Paths](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/map-paths.md): The Map Paths menu provides control over the flow of data from Data Asset to Capsule and between Capsules. It can be opened by clicking the gear icon ⚙️️ on any connection in the Pipeline.
- [Capsule Settings](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/capsule-settings.md): This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.
- [Pipeline Settings](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/pipeline-settings.md): The Pipeline Settings menu provides several options to customize how the Pipeline runs.
- [.codeocean](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/components-of-a-pipeline/.codeocean.md)
- [Managing Pipelines](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/managing-pipelines.md)
- [Queue Time & Compute Environment Utilization](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/managing-pipelines/queue-time-and-compute-environment-utilization.md)
- [Exporting Pipelines to your Local Machine](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/managing-pipelines/exporting-pipelines-to-your-local-machine.md): Steps for running code as you find it on Code Ocean locally.
- [Capsule vs Pipeline Differences](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/capsule-vs-pipeline-differences.md): Although Capsules generally function the same when run in a Pipeline, there are a few important differences which are outlined below.
- [How to Run Code in Parallel](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/how-to-run-code-in-parallel.md): This guide provides strategies, best practices, and considerations for parallelizing the execution of code that takes input parameters by using Capsules with App Panels in Pipelines.
- [Nextflow Configurations](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/nextflow-configurations.md): Explanation and examples of helpful Nextflow configurations.
- [Pipeline Monitoring](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/pipeline-monitoring.md)
- [Monitoring Dashboard](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/pipeline-monitoring/monitoring-dashboard.md)
- [Task Details](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/pipeline-monitoring/task-details.md)
- [Nextflow Artifacts](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/nextflow-artifacts.md)
- [nf-core Pipelines](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/nf-core-pipelines.md)
- [Import nf-core pipelines](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/nf-core-pipelines/import-nf-core-pipelines.md): A general introduction to importing from nf-core.
- [nf-core RNASeq Tutorial](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial.md)
- [iGenomes](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/nf-core-pipelines/nf-core-rnaseq-tutorial/igenomes.md): This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
- [Pipeline Tutorial](https://docs.codeocean.com/user-guide/v4.7.0/pipeline-guide/pipeline-tutorial.md): A video walkthrough of all Code Ocean Pipeline features.
- [Release Capsules and Pipelines](https://docs.codeocean.com/user-guide/v4.7.0/release-capsules-and-pipelines.md)
- [Creating and Using Release Capsules](https://docs.codeocean.com/user-guide/v4.7.0/release-capsules-and-pipelines/creating-and-using-release-capsules.md): A release Capsule is a permanently reproducible, run-only version, that is separate from the original. This enables your team to use a fully functioning version while you develop on the original.
- [Creating Release Pipelines](https://docs.codeocean.com/user-guide/v4.7.0/release-capsules-and-pipelines/creating-release-pipelines.md): A release Pipeline is an end-to-end reproducible version of your Pipeline that is saved in its current state and separate from the original.
- [Internal Releases](https://docs.codeocean.com/user-guide/v4.7.0/release-capsules-and-pipelines/internal-releases.md): The Internal Releases dashboard displays release Capsules and Pipelines that have been shared with the entire organization.
- [Collections](https://docs.codeocean.com/user-guide/v4.7.0/collections.md)
- [Code Ocean Apps](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps.md)
- [Genomics](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/genomics.md)
- [Cheminformatics](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/cheminformatics.md)
- [Visualization](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/visualization.md)
- [Machine Learning](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/machine-learning.md)
- [Data Connectors](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/data-connectors.md)
- [Quality Control](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/quality-control.md)
- [Use Cases and Examples](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/use-cases-and-examples.md): This section provides real world examples of how to use Apps Library Capsules for scientific tasks.
- [CombFold Pipeline](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/use-cases-and-examples/combfold-pipeline.md)
- [Data Connector Example](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/use-cases-and-examples/data-connector-example.md): This section explains how to use the Data Connector Capsules using Snowflake as an example.
- [Gene Set Enrichment Overview](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/use-cases-and-examples/gene-set-enrichment-overview.md): Introduction to the Gene Set Enrichment Analysis (GSEA) Capsule.
- [RNASeq Quantification Pipeline](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-apps/use-cases-and-examples/rnaseq-quantification-pipeline.md)
- [App Panel Guide](https://docs.codeocean.com/user-guide/v4.7.0/app-panel-guide.md): The App Panel enables researchers to interact with Capsules without editing Capsule code.
- [App Builder User Interface](https://docs.codeocean.com/user-guide/v4.7.0/app-panel-guide/creator-guide.md)
- [Validation pattern for strings](https://docs.codeocean.com/user-guide/v4.7.0/app-panel-guide/creator-guide/validation-pattern-for-strings.md)
- [Passing App Panel's Parameters to the Script](https://docs.codeocean.com/user-guide/v4.7.0/app-panel-guide/passing-app-panels-parameters-to-the-script.md)
- [Releasing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.7.0/app-panel-guide/releasing-an-app-panel-capsule.md)
- [Executing an App Panel Capsule](https://docs.codeocean.com/user-guide/v4.7.0/app-panel-guide/viewer-guide.md)
- [Aqua & Agents Guide](https://docs.codeocean.com/user-guide/v4.7.0/aqua-and-agents-guide.md)
- [Aqua](https://docs.codeocean.com/user-guide/v4.7.0/aqua-and-agents-guide/aqua.md)
- [Model Context Protocol (MCP)](https://docs.codeocean.com/user-guide/v4.7.0/aqua-and-agents-guide/model-context-protocol-mcp.md)
- [Cline](https://docs.codeocean.com/user-guide/v4.7.0/aqua-and-agents-guide/cline.md)
- [MLflow Guide](https://docs.codeocean.com/user-guide/v4.7.0/ml-flow.md): Learn all about native MLflow integration into Code Ocean.
- [Enable MLflow Tracking](https://docs.codeocean.com/user-guide/v4.7.0/ml-flow/enable-mlflow-tracking.md): Learn how to enable MLflow tracking in Capsules and Pipelines.
- [MLflow UI](https://docs.codeocean.com/user-guide/v4.7.0/ml-flow/mlflow-ui.md): Enter the MLflow UI from a Capsule or Pipeline to view the associated experiment or run.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.7.0/ml-flow/creating-models.md): Create a Code Ocean asset with lineage and provenance from your machine learning models.
- [MLflow Permissions](https://docs.codeocean.com/user-guide/v4.7.0/ml-flow/mlflow-permissions.md): Learn about MLflow permissions.
- [Models Guide](https://docs.codeocean.com/user-guide/v4.7.0/models-guide.md): Learn to create, use, and share Models in Code Ocean.
- [Creating Models](https://docs.codeocean.com/user-guide/v4.7.0/models-guide/creating-models.md): Create a Code Ocean Model by registering it in MLflow, creating from a Capsule or Pipeline result, or by importing from Hugging Face.
- [Managing Models](https://docs.codeocean.com/user-guide/v4.7.0/models-guide/managing-models.md)
- [Activity Center](https://docs.codeocean.com/user-guide/v4.7.0/activity-center.md)
- [Git Provider Integration Guide](https://docs.codeocean.com/user-guide/v4.7.0/git-provider-integration-guide.md): Learn to integrate a Capsule or Pipeline with an external Git repository
- [Setting up the Integration](https://docs.codeocean.com/user-guide/v4.7.0/git-provider-integration-guide/setting-up-the-integration.md)
- [Using Git Provider Integration](https://docs.codeocean.com/user-guide/v4.7.0/git-provider-integration-guide/github-integration-user-guide.md)
- [Code Ocean API](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api.md): The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application.
- [Authentication](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api/authentication.md): Code Ocean uses Access Tokens to authenticate requests. You can view and manage your access tokens from within your Dashboard under Access Tokens.
- [Errors](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api/errors.md): Code Ocean utilizes conventional HTTP response codes to indicate the success or failure of an API request.
- [Capsule](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api/capsule.md)
- [Computation](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api/computation.md)
- [Data Asset](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api/data-asset.md)
- [Python SDK](https://docs.codeocean.com/user-guide/v4.7.0/code-ocean-api/python-sdk.md): The Code Ocean Python SDK makes it even easier to leverage the full functionality of the extensive Code Ocean Public API in your Python scripts and applications.
- [More Support](https://docs.codeocean.com/user-guide/v4.7.0/more-support.md)

## Release Notes

- [Release Notes](https://docs.codeocean.com/user-guide/release-notes/release-notes.md)
- [Release Notes 4.7 (July 2026)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.7-july-2026.md)
- [Release Notes 4.6 (June 2026)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.6-june-2026.md)
- [Release Notes 4.5 (May 2026)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.5-may-2026.md)
- [Release Notes 4.4 (April 2026)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.4-april-2026.md)
- [Release Notes 4.3 (February 2026)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.3-february-2026.md)
- [Release Notes 4.2 (January 2026)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.2-january-2026.md)
- [Release Notes 4.1 (December 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.1-december-2025.md)
- [Release Notes 4.0 (November 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-4.0-november-2025.md)
- [Release Notes 3.9 (September 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.9-september-2025.md)
- [Release Notes 3.8 (September 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.8-september-2025.md)
- [Release Notes 3.7 (July 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.7-july-2025.md)
- [Release Notes 3.6 (May 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.6-may-2025.md)
- [Release Notes 3.5 (April 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.5-april-2025.md)
- [Release Notes 3.4 (March 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.4-march-2025.md)
- [Release Notes 3.3 (February 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.3-february-2025.md)
- [Release Notes 3.2 (February 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.2-february-2025.md)
- [Release Notes 3.1 (January 2025)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.1-january-2025.md)
- [Release Notes 3.0 (October 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-3.0-october-2024.md)
- [Release Notes 2.22 (August 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.22-august-2024.md)
- [Release Notes 2.21 (June 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.21-june-2024.md)
- [Release Notes 2.20 (May 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.20-may-2024.md)
- [Release Notes 2.19 (April 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.19-april-2024.md)
- [Release Notes 2.18 (March 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.18-march-2024.md)
- [Release Notes 2.17 (February 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.17-february-2024.md)
- [Release Notes 2.16 (January 2024)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.16-january-2024.md)
- [Release Notes 2.15 (November 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.15-november-2023.md)
- [Release Notes 2.14 (September 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.14-september-2023.md)
- [Release Notes 2.13 (July 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.13-july-2023.md)
- [Release Notes 2.12 (May 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.12-may-2023.md)
- [Release Notes 2.11 (April 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.11-april-2023.md)
- [Release Notes 2.10 (March 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.10-march-2023.md)
- [Release Notes 2.9 (January 2023)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-2.9-january-2023.md)
- [Release Notes v2.8 (December 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.8-december-2022.md)
- [Release Notes v2.7 (November 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.7-november-2022.md)
- [Release Notes v2.6 (September 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.6-september-2022.md)
- [Release Notes v2.5 (August 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.5-august-2022.md)
- [Release Notes v2.4 (July 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.4-july-2022.md): The new features that have been included in Code Ocean 2.4 are:
- [Release Notes v2.3 (June 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.3-june-2022.md): The new features that have been included in Code Ocean 2.3 are:
- [Release Notes v2.2 (May 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.2-may-2022.md)
- [Release Notes v2.1 (April 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.1-april-2022.md)
- [Release Notes v2.0 (March 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v2.0-march-2022.md)
- [Release Notes v1.20 (February 2021)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v1.20-february-2021.md)
- [Release Notes v1.19 (January 2022)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v1.19-january-2022.md)
- [Release Notes v1.18 (December 2021)](https://docs.codeocean.com/user-guide/release-notes/release-notes/release-notes-v1.18-december-2021.md): The new features that have been included in Code Ocean 1.18 release are:


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## Querying This Documentation
If you need additional information, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on a page URL with the `ask` query parameter:
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The question should be specific, self-contained, and written in natural language.
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Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.