Collections

Collections is a feature within the Code Ocean computational science platform that enables research teams to gather and organize their computational assets — including Compute Capsules, Pipelines, no-code Apps, and Data — by project or scientific area of interest. Designed for life sciences organizations, Collections makes it straightforward to surface and share reproducible work across teams, improving visibility, accessibility, and reusability of critical computational resources.

Collections is built for computational scientists, R&D leadership, bench scientists, and IT teams who need a structured, governed way to browse and discover what computational work is available within their organization — or to share curated work publicly beyond it.

Key Capabilities

• Organize computational assets: Owners of released versions of Compute Capsules, Pipelines, Apps, and Data can add them to Collections within their organization. Admin-defined Collections trees enforce a consistent folder structure across the organization.
• Centralized discoverability: Collections make it straightforward to organize everything in one place, so the wider organization can easily see what computational work is available and find what they need without friction.
• Public Collections: Teams can create publicly accessible, curated Collections of Capsules, Pipelines, Apps, Models, and Data Assets to boost visibility and share reproducible work beyond the organization.

How Collections Organizes the Code Ocean Platform

• Compute Capsules: Categorize and surface release versions and gold-standard Compute Capsules into their relevant project areas, making them easy to find and reuse.
• Pipelines: Make released Pipelines visible and accessible to the wider organization, browsable by subject area.
• Data: Make data findable, accessible, and easier to reuse and reproduce across different areas and within different projects.

Access Control and Governance

• Every asset within a Collection retains its own individual access permissions — users will only see assets they have permission to view.
• Only the owner or owners of an asset can add or remove it from a Collection.
• Capsules, Pipelines, and Apps that are not yet released or are still in development cannot be added to a Collection, ensuring that only assets that have passed important quality checks are included.
• Administrators determine the Collections folder structure for the entire organization, enforcing consistent governance.

Broader Platform Capabilities for Computational Science

• Data analysis: Use ready-made template Compute Capsules, develop workflows in preferred languages and IDEs with any open-source software, and leverage built-in containerization to guarantee reproducibility.
• Data management: Manage organizational data with access controls, custom metadata, and controlled vocabularies built to meet all FAIR principles, ensuring consistency and improving searchability.
• Bioinformatics pipelines: Build, configure, and monitor pipelines using a visual builder, or import from nf-core in one click. Pipelines run on AWS Batch out-of-the-box for automatic scaling with no setup required.
• ML model development: Supports AI, ML, 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 ranging from individual files to petabyte-scale datasets using dedicated desktop applications or custom deep learning pipelines, with no DevOps required.
• Cloud management: Easily manage data and provision CPUs, GPUs, and RAM. Spot instances, idleness detection, and automated shutdown help reduce cloud costs.
• Data and model provenance: Automated result provenance and lineage graph generation provide a visual representation of every Capsule, Pipeline, and Data asset involved in a computation, supporting reproducibility assessment.

Collections is part of the broader Code Ocean platform, which is deployed in the cloud and integrates with AWS Batch, MLflow, and nf-core, among other tools. The platform is designed to support the full computational science lifecycle for biotech and pharmaceutical organizations.