Release Notes 4.0 (November 2025)

Aqua AI Agent

Aqua is Code Ocean's dedicated AI agent, powered by Anthropic’s Sonnet 4.

Pre-configured with the Code Ocean Model Context Protocol (MCP) and AWS Bedrock integration, Aqua acts safely and securely inside your workspace using each users' unique permissions, allowing any user to find, edit, troubleshoot, and run analyses using only natural language.

By default, Aqua will not be enabled during upgrade. Admins can learn more about how to enable Aqua along with important prerequisites and considerations in our Admin Guide here.

MCP Server

The Code Ocean public MCP server allows AI agents to work securely and perform actions in Code Ocean. The MCP is integrated with Aqua out-of-the-box, and can be installed in popular tools like Github Copilot, Cline, Claude Desktop, Cursor, Windsurf and more.

Capsules - Cline Integration

Every Capsule includes the Cline coding agent, powered by secure access to AWS Bedrock. You can access Cline in the VS Code [code-server] Cloud Workstation as shown below.

App Panel - Apply Parameters from Previous Run

Users can now quickly apply App Panel parameter values from a previous run directly to the App Panel by clicking "Apply to App Panel". This feature streamlines parameter setup, and works for runs initiated in the UI after this version's release.

Post-Run Automation & Capsule Settings Panel

Capsules and Pipelines can now be configured with post-run automations that will trigger once a run has been completed. This feature streamlines post-run workflows such as data creation, metadata updates, and asset sharing.

Key Highlights:

• A new Capsule Settings panel that includes Credentials, Automation, and MLflow.

• The Automation tab in Capsule and Pipeline settings where users set the Automation Capsule and configure whether to run only upon success or always.

• The Timeline will show clear deep linking between runs: "Open Automation Run" and "Automated From".

Capsules - VS Code [code-server] Package Manager

A new Code-Server package manager is available in Capsules when Code-Server is detected in the environment, improving ease of use and reliability when installing VS Code extensions.

Collections Enhancements

We've made improvements to key aspects of working with Collections:

• Adding assets to collections: You can now add assets to Collections from multiple new places, including dashboards, Data/Model details, the Capsule/Pipeline IDE header, and the newly released asset modal.

• Using assets exported from Collections: The instructions in the REPRODUCING.md file of exported public assets have been improved to better guide Public Collections users how to access and use data locally.

1-Step SAML Login

We have simplified login for VPC deployments by enabling 1-step SAML SSO (email input no longer required) and removing the sign-up link.

Custom Metadata Enhancements

We're making Custom Metadata more powerful with two major improvements:

• Key Categories: By grouping keys into categories, metadata can now be tailored to specific teams, projects, and analyses.

• Multiple Values: Admins can enable multiple values for a key, increasing the functionality and flexibility of Custom Metadata.

Pipelines - Cloud Workstations for Custom Pipelines

Users can now launch VS Code [code-server] and Terminal Cloud Workstations directly within custom Pipelines, providing a full-featured environment for Pipeline development.

Coming soon: Run custom Pipelines directly inside Cloud Workstations.

Pipelines - Compute Resource tab in Pipeline Settings

Pipeline instance type configuration (On Demand vs. Spot) has been moved from the General tab of the Pipeline Settings to a new Compute Resource tab. This is also where you can select the compute resource for Cloud Workstations in custom pipelines.

Code Ocean Public API - Additions & Enhancements

Python SDK - v0.12.0

All of the Public API updates below have been reflected in version 0.12.0 of the Code Ocean Python SDK. You can learn more about the Code Ocean Python SDK in our User Guide here and on Github here.

Get Result File URLs

This new endpoint allows for the generation of two URLs to a Computation result file:

• download_url - signed URL for downloading the file

• view_url - signed URL for viewing the file in the browser

Request Example

curl https://{domain}/api/v1/computations/9390055d-7884-4997-8dfc-88bf7445b617/results/urls?path=GSM12345_R1_fastqc.html \
   -u "cop_d23dasd312":

The previous Get Result File Download URL endpoint is deprecated but will be supported until August 2026.

Get Data Asset File URLs

This new endpoint allows for the generation of two URLs to a file in an Internal Data Asset:

• download_url - signed URL for downloading the file

• view_url - signed URL for viewing the file in the browser

Request Example

curl -H "Content-Type: application/json" -u ${CUSTOM_KEY}: -X GET https://${co_domain}/api/v1/data_assets/${data_asset_id}/files/urls?path=${path_to_file}

The previous Get Data Asset File Download URL endpoint is deprecated but will be supported until August 2026.

Capsule Object - last_accessed field added

The Capsule object now includes a last_accessed field which indicates the last date any user accessed the Capsule.

Get Capsule App Panel

A new endpoint has been added which provides all of the details of a Capsule or Pipeline's App Panel, including default parameter values. In Pipelines of Capsules, the response will also include pipeline process names and their corresponding App Panels.

Request Example

curl -H "Content-Type: application/json" -u ${CUSTOM_KEY}: -X GET https://${co_domain}/api/v1/capsules/${capsule_id}/app_panel

Response

• general (optional) general information

  • title string (optional)

  • instructions string (optional)

  • help_text string (optional)

• data_assets array (optional)

  input data assets

  • id string data asset ID

  • mount string data asset mount within the capsule’s/pipeline’s data folder

  • name string data asset name

  • description string (optional) data asset description

  • help_text string (optional) additional help text

  • kind - data assets type - internal, external or combined

  • accessible - boolean - indicates whether the data asset is accessible to the user

• categories array (optional) parameter categories (N/A for pipelines of capsules)

  • id string category ID

  • name string category name

  • description string (optional) category description

  • help_text string (optional) additional help text

• parameters array (optional) input parameters (N/A for pipelines of capsules)

  • category string (optional) category id from the category list, in case parameters are divided into categories

  • name string parameter label

  • param_name string (optional) parameter name

  • description string (optional) category description

  • help_text string (optional) additional help text

  • type string parameter type text, list or file

  • value_type string (optional) the type of the parameter value

  • default_value string (optional) default parameter value

  • required boolean (optional) indicates a required parameter

  • hidden boolean (optional) indicates a hidden parameter

  • minimum float64 (optional) minimum numeric value

  • maximum float64 (optional) maximum numeric value

  • pattern string (optional) value validation pattern

  • value_options array (optional) list of value options for list parameters

• results array (optional) selected result files

  • file_name string result file name

• processes array (optional) pipeline process names and their corresponding app panels (for pipelines of capsules only)

  • name string process name

  • categories array (optional) parameter categories

  • parameters array (optional) input parameter

Archive Capsule

A new endpoint has been introduced to archive Capsules via the Code Ocean Public API.

Request Example

curl -H "Content-Type: application/json" -u ${CUSTOM_KEY}: -X PATCH https://${co_domain}/api/v1/capsules/${capsule_id}/archive

Delete Capsule

This new endpoint allows for the deletion of archived Capsules via the Code Ocean Public API.

Request Example

curl -H "Content-Type: application/json" -u ${CUSTOM_KEY}: -X DELETE https://${co_domain}/api/v1/capsules/${capsule_id}

Admin - Extend Cloud Workstation Idle Time

Admins can set a custom default idle shutdown time for Cloud Workstations (previously fixed at 2 hours). Admins can also choose to allow users to extend idle time on a per-session basis, providing more flexibility for long-running work.

These controls give teams greater flexibility to keep long-running sessions active without interruptions or delays.

Admin - Maintenance Mode Improvements

We have improved system job handling with clearer distinction between Maintenance and System Initialization tasks and improved error messages to provide more actionable information.