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Apps Light@8x

Apps

Browse a selection of ready-to-use bioinformatics Apps, and take advantage of functionality to transform computational work into no-code Apps for others to use.

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Key capabilities

Access a library of ready-made bioinformatics Apps

Get started faster with ready-made Apps to use in your workflows. Includes Apps for genomics, generative AI, cheminformatics, visualization, machine learning, data connections, and quality control.

Read more about pre-built Apps
ready-made-bioinformatics-apps

Release Capsules and Pipelines as no-code Apps

Compute Capsules and Pipelines can be adapted into paramaterized Apps for distribution throughout the rest of the organization, including to non-coders.

Read more about the app builder
release-as-no-code-apps

Use built-in data visualization tools

Code Ocean integrates Streamit, RShiny, and Integrative Genomics Viewer (IGV). Launch cloud workstations with one click from any Compute Capsule.

Read more about visualization
visualization-tools

How Apps work with the rest of the platform

Capsules Colour@8x Turn Compute Capsules into Apps

Make computational work available across the wider organization for use by non-coding researchers.

 Capsules
CapsulesGB
Pipeline Colour@8x Create no-code bioinformatics pipelines

Transform your bioinformatics pipelines into accessible, parameterized Apps accessible to others, including non-coders. 

 Pipelines
Pipelines
Collections@8x Add Apps to different Collections

Make Apps accessible and visible to the rest of the organization by organizing them into different Collections.

 Collections
Collections

Frequently asked questions

Apps Colour@8xApps

What options are available for making apps?

There are three options. Streamlit and RShiny are both available as cloud workstations. Any Capsule or Pipeline can also be converted into an app with the app panel.

Can you make apps out of both Capsules and Pipelines?

Yes. Any Capsule or Pipeline can be converted into a parameterized no-code App that can then be released for use by non-coders.

Can non-coding users bring their own data to use in an App?

Yes. Users can easily swap out App data for their own in an App Panel. This is also possible with Streamlit and RShiny.

Are there readymade apps already available in the platform?

Yes. You can find more information about this and a full list of apps in our documentation.

Do you ever add new apps to this list?

We often add new apps, usually at the request of existing customers. To find out if we can help you with this, please get in touch.

Built for Computational Science

  • Data analysis

    data-analysis
    Compute Scalability@8x

    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
    Data Management Light@8x

    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

    bioinformatic-pipelines
    Pipelines Light@8x

    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.

  • ML models

    AI-MLflow
    Data Analysis Light@8x

    ML model development

    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
    Multiomics Light@8x

    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.

  • Imaging

    image-processing
    Image processing Light@8x

    Imaging

    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
    Cloud management Light@8x

    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. 

  • Data/model provenance

    result-provenance
    Provenance Light@8x

    Data/model 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
Compute Scalability@8x

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 Light@8x

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.

bioinformatic-pipelines
Pipelines Light@8x

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-MLflow
Data Analysis Light@8x

ML model development

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 Light@8x

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 Light@8x

Imaging

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 Light@8x

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
Provenance Light@8x

Data/model 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.

Join thousands of other Computational Scientists using Code Ocean

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