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September 3, 2021

Making Jupyter Notebooks a Research Collaboration Environment

Jupyter Notebooks have become exceedingly popular in computational biology because of their ability to combine code, images and text into a single document. Adding detailed as well as easy to understand descriptions of a computational workflow is very helpful when the team has knowledge gaps, where members have different levels of coding experience and skills.

Despite their many advantages, Jupyter Notebooks also have drawbacks: they can get messy when others try to edit or reproduce work. This “messiness” can very easily lead to so many conflicting versions among users that shareability, traceability and reproducibility are all out of sight.

This is the problem we are solving with our Code Ocean computational platform:  Compute Capsules allow users to share data, code and results in a research environment specifically designed to allow seamless collaboration. This creates traceable and reproducible notebooks easily shared among a team through the Computational Workbench.

This video introduces through three views for how Capsules promote collaboration: Creating a Compute Capsule to share for collaboration, viewing a shared Compute Capsule for collaboration and presenting completed Compute Capsules through the Explore Page.


For more information about the Code Ocean platform please go to or go to /explore to view public research Compute Capsules.

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