Code Ocean

Code Ocean is a reproducible and traceable computational science platform designed for collaborative research in the cloud. Trusted by thousands of computational scientists across biotech and pharma, Code Ocean addresses the core challenges of modern life science R&D: the difficulty of reproducing results across compute environments, the pain of manual processes and bespoke systems, and the friction of collaboration within and between computational teams. Version 4.0, dubbed Trusted Agents, extends the platform with agentic AI workflows that generate reproducible, compliant results for both humans and AI.

Code Ocean installs into existing cloud architectures and serves a broad range of users — from computational scientists and bench scientists to IT and engineering teams and R&D leadership — providing a unified environment that eliminates the need for custom-built infrastructure and reduces costly technical debt.

Core Product Modules

• Aqua: A generative AI capability that accelerates computational workflows securely, forming the foundation of the platform's agentic features in version 4.0.
• Compute Capsules: Self-contained units that encapsulate code, data, environment configuration, and generated results, enabling full reproducibility and portability across compute environments.
• Pipelines: Tools to connect, automate, parallelize, and scale computational work, supporting everything from straightforward analyses to complex bioinformatics pipelines.
• Data: A centralized layer for managing all data in the cloud and from external sources in a single place.
• Models: A unified environment for machine learning models with native MLflow integration.
• Lineage Graph: An automated, immutable record of result data provenance, giving researchers full visibility into how every result was generated.
• Collections: Functionality to gather and organize computational work, making it visible and findable across teams.
• Apps: Ready-made bioinformatics applications that bench scientists can use without writing code, with the ability to quickly build custom apps as well.
• Admin Panel: A single pane of glass for IT and engineering teams to manage all users, resources, and data across the deployment.
• API: Programmatic access to the platform without requiring use of the user interface.

Core Platform Capabilities

• Cloud environment provisioning: Built-in tools and automated Dockerfile generation make it easy to build and configure environments. Users can develop in their preferred cloud workstation, attach data of any size, deploy to the cloud in one click, and shut down automatically when idle.
• Collaboration: Teams can share and co-develop any Compute Capsule, Pipeline, or Data asset within their deployment, eliminating environment inconsistency and enabling global teams to work together effectively.
• Reproducibility and traceability: All development is tracked with Git, and the Lineage Graph preserves everything needed for full reproducibility. There is no vendor lock-in — users can export anything at any time and run it in any other environment.
• No-code access: Bench scientists and non-programmers can access powerful bioinformatics analyses and pipelines through ready-made Apps without requiring engineering support.
• Scalability: The platform is designed to automate and scale major aspects of the research process, with customers reporting workflow speed improvements of 10x or more.

Why Reproducibility Matters

• An estimated $28 billion is spent annually on non-reproducible preclinical research.
• 74% of publicly available R files fail to run without errors.
• 97% of Jupyter notebooks are not reproducible as documented.
• Reproducibility and traceability are critical not only for scientific progress but also for quality assurance, publications, mergers and acquisitions, and FDA compliance.

Open Science Library (OSL)

• Code Ocean operates the Open Science Library, which serves both authors and publishers as the industry standard for computational research integrity.
• OSL for Authors provides login, sign-up, documentation, and support for researchers seeking to publish reproducible computational work.
• OSL for Publishers positions Code Ocean as the trusted standard for ensuring the integrity of computational research in academic and scientific publishing.

Notable Customers and Testimonials

• CytoReason: Code Ocean enables automation and scaling of major research processes, allowing scientists to focus on core competencies and achieve higher goals.
• Lantern Pharma: The platform enabled the entire team to work together in a shared environment, with pipeline development cited as the biggest win.
• Allen Institute: Self-service capabilities allow scientists to work reproducibly with minimal support, freeing engineers to focus on domain-specific challenges.
• Princess Margaret Cancer Centre: Code Ocean is credited with solving tracking and reproducibility of analysis for researchers and increasing trust in results.
• Ochre Bio: The platform accelerated internal image pre-processing computational workflows by at least 10x, improving collaboration between global teams and removing the need for complex cloud infrastructure setup.

Founded by researchers turned entrepreneurs — including co-founders Simon Adar (CEO) and Ram Dayan (CTO), both with deep backgrounds in scientific computing and software engineering — Code Ocean's mission is to champion the computational scientist and provide the industry standard platform for computational life science R&D.