API

The Code Ocean API enables programmatic access to the Code Ocean computational science platform without requiring use of the web interface. Built around REST principles, it accepts and returns JSON-encoded request bodies and responses, and uses standard HTTP response codes, authentication methods, and verbs for seamless programmatic interaction.

The API is designed for engineering teams, bioinformatics and data science groups, platform teams, and anyone who needs reproducible research workflows embedded in their own tools and systems. It exposes core platform functionality including running Computations, creating and managing Data Assets, automating Capsules and Pipelines, programmatically provisioning compute, collecting results, and retrieving metadata.

Key API Capabilities

• Automate computational workflows: Use the API to automate Capsules, Pipelines, and Data Assets within Code Ocean, reducing manual intervention and enabling scalable, repeatable processes.
• Connect multiple data sources and targets: Programmatically interact with the platform to integrate data from multiple sources and direct outputs to desired targets.
• Find data and analyses: Programmatically locate datasets, Capsules, or associated results to accelerate discovery and collaboration across projects.
• Interface with Compute Capsules: Get metadata, list Computations, and attach or detach Data Assets from individual or multiple Capsules.
• Automate Pipeline execution at scale: Use the API to automate bioinformatics pipelines for upstream data processing at scale.

Technical Details

• The API is organized around REST with predictable resource-oriented URLs.
• All requests and responses are JSON-encoded.
• Standard HTTP verbs, authentication, and status codes are used throughout.
• Access tokens can be viewed and managed from within the Account page under Access Tokens.
• A Python SDK is available as a wrapper over the public API, making it easy to leverage full API functionality from Python scripts and applications.

Platform Capabilities Accessible via API

• Data analysis: Leverage ready-made template Compute Capsules, develop workflows in preferred languages and IDEs using open-source software, with built-in containerization to guarantee reproducibility.
• Data management: Manage organizational data and access controls, with support for FAIR principles, custom metadata, and controlled vocabularies to ensure consistency and searchability.
• Bioinformatics pipelines: Build, configure, and monitor pipelines using a visual builder, import from nf-core in one click, and run on AWS Batch out-of-the-box for automatic scaling with no setup required.
• ML model development: Support for AI, Machine Learning, Deep Learning, and Generative AI workflows, with GPU-ready environments, MLflow integration for model tracking and lifecycle management, and out-of-the-box reproducibility and lineage.
• Multiomics: Analyze large multimodal datasets using scalable compute and storage, cached R and Python packages, and preloaded multiomics analysis software with full lineage and reproducibility.
• Imaging: Process images using dedicated desktop applications or custom deep learning pipelines, from individual files to petabyte-scale datasets, with no DevOps required.
• Cloud management: Manage CPUs, GPUs, and RAM; assign flex and dedicated machines; and reduce cloud costs with spot instances, idleness detection, and automated shutdown.
• Data and model provenance: Track all data and results with automated result provenance and lineage graph generation, providing a visual representation of every Capsule, Pipeline, and Data Asset involved in a computation.

The Code Ocean API integrates tightly with the broader Code Ocean platform, including Compute Capsules, Pipelines, Data Assets, and the Lineage Graph, making it a powerful tool for embedding reproducible computational science workflows into existing organizational infrastructure and tooling.