Compute Capsules
A shareable, traceable, reproducible encapsulation of the code, data, and environments used in computational research, version controlled and linked to the results they produce.
Key capabilities
Set up environments with automated Dockerfile generation
Choose your environment and add packages while the Capsule automatically writes your Dockerfile. Work with the included base images or import your own. Optionally unlock the Dockerfile to customize your script.
Provision and manage compute resources
Select from Flex compute options, or choose a dedicated EC2 instance with optional spot instance selection. Instances automatically terminate when idle for 2 hours. No compute cost pass-through: Code Ocean installs in your AWS cloud environment.
Launch cloud workstations
Choose from a selection of integrated IDEs and virtual machines to begin developing within your Capsule. Includes: JupyterLab, RStudio, Jupyter Notebook, Shiny, MATLAB, VS Code, Streamlit, Ubuntu Desktop, and IGV.
Track everything with automated Git
Everything developed in a Capsule gets automatically tracked with Git without the user having to know Git or set it up—everything is automated. Connects to GitHub, GitLab, Bitbucket, or Azure DevOps.
Share your work with other users or groups
Share Capsules with other users or groups on your team with user permissions built-in. Work on the Capsule collaboratively, or clone and adapt for your own needs. Option to share all assets associated.
How Capsules work with the rest of the Code Ocean platform
Assemble Capsules into Pipelines
Pipelines
Organize different projects into Collections
Collections
Track result provenance with Lineage Graph
Lineage Graph
Built for bioinformatics
-
Data analysis
Data analysis
Use ready-made template Compute Capsules to analyze your data, develop your data analysis workflow in your preferred language and IDE using any open-source software, and take advantage of built-in containerization to guarantee reproducibility.
-
Data management
Data management
Manage your organization's data and control who has access to it. Built specifically to meet all FAIR principles, data management in Code Ocean uses custom metadata and controlled vocabularies to ensure consistency and improve searchability.
-
Bioinformatics pipelines
Bioinformatics pipelines
Build, configure and monitor bioinformatics pipelines from scratch using a visual builder for easy set-up. Or, import from nf-core in one click for instant access to a curated set of best practice analysis pipelines. Runs on AWS Batch out-of-the-box, so your pipelines scale automatically. No setup needed.
-
AI & Machine Learning
AI & Machine Learning
Code Ocean is uniquely suited for Artificial Intelligence, Machine Learning, Deep Learning, and Generative AI. Install GPU-ready environments and provision GPU resources in a few clicks. Integration with MLFlow allows you to develop models, track parameters, manage models from development to production, while enjoying out-of-the-box reproducibility and lineage.
-
Multiomics
Multiomics
Analyze and work with large multimodal datasets efficiently using scalable compute and storage resources, cached packages for R and Python, preloaded multiomics analysis software that works out of the box and full lineage and reproducibility.
-
Image processing
Image processing
Process images using a variety of tools: from dedicated desktop applications to custom-written deep learning pipelines, from a few individual files to petabyte-sized datasets. No DevOps required, always with lineage.
-
Cloud management
Cloud management
Code Ocean makes it easy to manage data and provision compute: CPUs, GPUs, and RAM. Assign flex machines and dedicated machines to manage what is available to your users. Spot instances, idleness detection, and automated shutdown help reduce cloud costs.
-
Result provenance
Result provenance
Keep track of all data and results with automated result provenance and lineage graph generation. Assess reproducibility with a visual representation of every Capsule, Pipeline, and Data asset involved in a computation.
Data analysis
Use ready-made template Compute Capsules to analyze your data, develop your data analysis workflow in your preferred language and IDE using any open-source software, and take advantage of built-in containerization to guarantee reproducibility.
Data management
Manage your organization's data and control who has access to it. Built specifically to meet all FAIR principles, data management in 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 for easy set-up. Or, import from nf-core in one click for instant access to a curated set of best practice analysis pipelines. Runs on AWS Batch out-of-the-box, so your pipelines scale automatically. No setup needed.
AI & Machine Learning
Code Ocean is uniquely suited for Artificial Intelligence, Machine Learning, Deep Learning, and Generative AI. Install GPU-ready environments and provision GPU resources in a few clicks. Integration with MLFlow allows you to develop models, track parameters, manage models from development to production, while enjoying out-of-the-box reproducibility and lineage.
Multiomics
Analyze and work with large multimodal datasets efficiently using scalable compute and storage resources, cached packages for R and Python, preloaded multiomics analysis software that works out of the box and full lineage and reproducibility.
Image processing
Process images using a variety of tools: from dedicated desktop applications to custom-written deep learning pipelines, from a few individual files to petabyte-sized datasets. No DevOps required, always with lineage.
Cloud management
Code Ocean makes it easy to manage data and provision compute: CPUs, GPUs, and RAM. Assign flex machines and dedicated machines to manage what is available to your users. Spot instances, idleness detection, and automated shutdown help reduce cloud costs.
Result provenance
Keep track of all data and results with automated result provenance and lineage graph generation. Assess reproducibility with a visual representation of every Capsule, Pipeline, and Data asset involved in a computation.
