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Computational Scientists
Cloud-based, collaborative bioinformatics for computational research
Code Ocean makes it easy for computational scientists and bioinformaticians to perform analysis, build pipelines, and reproduce their results in a secure cloud-based environment.
Key benefits for computational scientists
Get started in the cloud in minutes
Code Ocean makes it easy to work in the cloud. Attach data from your S3 buckets to any Compute Capsule or Pipeline, assign a flex or dedicated compute resource, then start development in your preferred IDE and any open source language like R or Python.
Build pipelines in Nextflow without writing code
Build in a visual editor while Code Ocean writes Nextflow in the background in real-time. Import pre-existing pipelines directly from nf-core, clone from a Git repo, or unlock to write your own Nextflow. Runs on a preconfigured AWS Batch instance to parallelize compute and scale storage with EBS autoscaling.
Collaborate with other colleagues and teams
Share everything from basic analyses to complex pipelines with individual users or whole groups within your organization. Assign permissions to co-develop, or let them duplicate and take things in a new direction.
Import existing work from your Git provider
Code Ocean connects to multiple different git providers. New Capsules and Pipelines in Code Ocean can be created by duplicating code from private or public git sources to run within your Code Ocean deployment.
Automate result provenance & traceability
All Result Data include a lineage graph showing data sources and processing steps. All runs are captured in the Timeline and all development is tracked by Git, which can be optionally synced with your preferred provider.
What organizations use Code Ocean?
Biotechs
Pharma companies
Research institutes
What our customers say:
“Code Ocean sped up our internal image pre-processing computational workflow by at least 10x, improving collaboration and productivity between our global teams ... removing the need for painful cloud computing infrastructure set up.”
What our customers say:
“Code Ocean's self-service capabilities make it easy for our scientists to do their work reproducibly. New users to the platform can get far with just a little support, giving our engineers time to focus on domain-specific challenges.”
What our customers say:
“Code Ocean totally solves tracking and reproducing analysis for researchers and increases trust in the results.”
Key product features
Compute Capsules
Capsules
Pipelines
Pipelines
Models
Models
Data
Data
Lineage Graph
Lineage Graph
Collections
Collections
Apps
Apps
Admin
Admin Panel
Built for Computational Science
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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.
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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.
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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.
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ML models
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.
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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.
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Imaging
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.
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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.
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Data/model provenance
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
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.
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
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
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.
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.
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