Compute Capsules

Compute Capsules, part of the Code Ocean platform, are shareable, traceable, and reproducible encapsulations of the code, data, and environments used in computational research. Version controlled and linked to the results they produce, Compute Capsules create an immutable record of every computational workflow — ensuring that whatever runs today will always run in the future. They are designed for computational scientists, R&D teams, and life sciences organizations that need to guarantee reproducibility and traceability across their research.

Compute Capsules support virtually any computational task, from simple exploratory data analysis and machine learning model training to building visualization apps and creating API connections — all while attaching data of any size, provisioning cloud compute, and co-developing with colleagues, with an automatically traceable and reproducible record of work maintained throughout.

Key Capabilities

• Automated Dockerfile generation: Choose your environment and add packages while the Capsule automatically writes your Dockerfile. Work with included base images or import your own, and optionally unlock the Dockerfile to customize your script directly.
• Flexible compute provisioning: Select from Flex compute options or choose a dedicated EC2 instance with optional spot instance selection. Instances automatically terminate after two hours of idle time. Code Ocean installs in your own AWS cloud environment with no compute cost pass-through.
• Cloud workstations: Launch integrated IDEs and virtual machines directly within your Capsule, including JupyterLab, RStudio, Jupyter Notebook, Shiny, MATLAB, VS Code, Streamlit, Ubuntu Desktop, and IGV.
• Automated Git version control: All development within a Capsule is automatically tracked with Git, requiring no prior Git knowledge or setup from the user. Native integrations are available for GitHub, GitLab, Bitbucket, and Azure DevOps.
• Sharing and collaboration: Share Capsules with individual users or groups with built-in user permissions. Collaborate on a Capsule directly, or clone and adapt it for individual needs, with the option to share all associated assets.

Use Cases for Computational Science

• Data analysis: Use ready-made template Compute Capsules to analyze data, develop workflows in your preferred language and IDE using any open-source software, and leverage built-in containerization to guarantee reproducibility.
• Data management: Manage organizational data and control access. Built to meet all FAIR principles, Code Ocean uses custom metadata and controlled vocabularies to ensure consistency and improve searchability.
• Bioinformatics pipelines: Build, configure, and monitor bioinformatics pipelines from scratch using a visual builder, or import from nf-core in one click for instant access to curated best-practice analysis pipelines. Runs on AWS Batch out-of-the-box for automatic scaling with no setup required.
• ML model development: Suited for AI, machine learning, deep learning, and generative AI workflows. Install GPU-ready environments and provision GPU resources in a few clicks. MLflow integration supports model development, parameter tracking, and model management from development to production with built-in reproducibility and lineage.
• Multiomics: Analyze large multimodal datasets using scalable compute and storage, cached packages for R and Python, and preloaded multiomics analysis software with full lineage and reproducibility.
• Imaging: Process images using dedicated desktop applications or custom deep learning pipelines, handling datasets ranging from individual files to petabyte-scale, with no DevOps required and full lineage tracking.
• Cloud management: Manage CPUs, GPUs, and RAM; assign flex and dedicated machines; and reduce cloud costs through 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.

Integration with the Code Ocean Platform

• Pipelines: Assemble Capsules into Nextflow-based Pipelines that run on AWS Batch to scale and automate computational workflows.
• Collections: Organize Capsules, Pipelines, Data, and Apps into Collections to improve findability across computational teams.
• Lineage Graph: Every result in Code Ocean includes an immutable, automated record of how it was created, enabling full provenance tracking.
• Data management: Data and Capsules are managed separately, allowing the same data asset to be attached to multiple Capsules simultaneously, reducing duplication and total cost of ownership. There is no file size limit for data attached to a Capsule.

Compute Capsules are deployed within your own AWS cloud environment, ensuring data sovereignty and eliminating vendor lock-in. The platform is built for life sciences organizations — including pharmaceutical, biotech, and academic research teams — seeking enterprise-grade reproducibility, compliance-readiness, and scalable computational infrastructure.