Apps

Code Ocean Apps is a feature of the Code Ocean computational science platform designed to make powerful bioinformatics analyses accessible to the entire research organization — including non-coding bench scientists. It combines a library of ready-made bioinformatics Apps with tools that allow computational scientists to transform their own Compute Capsules and Pipelines into parameterized, no-code Apps for broader distribution.

Apps is built for life sciences organizations that need to bridge the gap between computational and non-computational researchers, enabling self-service access to complex analyses without requiring coding expertise from end users.

Ready-Made Bioinformatics App Library

• Access a curated selection of pre-installed, ready-to-use bioinformatics Apps to accelerate workflows without starting from scratch.
• The library spans multiple domains including genomics, generative AI, cheminformatics, visualization, machine learning, data connections, and quality control.
• New Apps are regularly added to the library, often in response to requests from existing customers.

No-Code App Builder

• Any Compute Capsule or Pipeline on the platform can be converted into a parameterized no-code App using the built-in app panel.
• Apps built this way can be distributed across the wider organization for use by non-coding researchers.
• Non-coding users can bring their own data to use within an App by easily swapping out data in the App Panel.
• Three options are available for building Apps: Streamlit, RShiny (both available as cloud workstations), and the native app panel for converting any Capsule or Pipeline.

Built-In Data Visualization Tools

• Code Ocean integrates Streamlit, RShiny, and Integrative Genomics Viewer (IGV) as visualization tools.
• Cloud workstations can be launched with a single click from any Compute Capsule, enabling interactive data exploration.

How Apps Integrate with the Rest of the Platform

• Compute Capsules: Capsules can be turned into Apps to make computational work available across the wider organization, including to non-coding researchers.
• Pipelines: Bioinformatics pipelines can be transformed into accessible, parameterized Apps that non-coders can use directly.
• Collections: Apps can be added to Collections to make them visible, organized, and findable across the organization.

Broader Platform Capabilities Supporting Apps

• Data analysis: Ready-made template Compute Capsules support data analysis in any preferred language and IDE, with built-in containerization for reproducibility.
• Data management: Organizational data is managed in compliance with FAIR principles, using custom metadata and controlled vocabularies for consistency and searchability.
• Bioinformatics pipelines: Pipelines can be built visually from scratch or imported from nf-core in one click, running on AWS Batch for automatic scaling.
• ML model development: GPU-ready environments and MLflow integration support AI, ML, deep learning, and generative AI workflows with full reproducibility and lineage tracking.
• Multiomics: Large multimodal datasets can be analyzed using scalable compute and storage, with preloaded multiomics software and full lineage support.
• Imaging: Image processing is supported across a range of tools and scales, from individual files to petabyte-sized datasets, with no DevOps required.
• Cloud management: CPU, GPU, and RAM provisioning is managed through a single interface, with spot instances, idleness detection, and automated shutdown to control costs.
• Data and model provenance: Automated lineage graph generation provides a visual record of every Capsule, Pipeline, and Data asset involved in any computation.

Code Ocean Apps is part of a broader cloud-based platform designed for computational science in biotech and pharma. It supports deployment in virtual private cloud (VPC) environments and integrates with external tools including MLflow, nf-core, AWS Batch, Streamlit, RShiny, and IGV, making it suitable for enterprise R&D organizations seeking reproducibility, traceability, and scalable self-service access to bioinformatics capabilities.