Video Library
A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
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A collection of tutorials and demos to help new users familiarize themselves with the system and its primary functionality.
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A quick overview of the Code Ocean platform, it's key features, and example workflows.
You can learn more about each individual feature in the videos below and in their respective guides.
An introduction to the foundational object for working with data in Code Ocean.
A key reproducibility feature in Code Ocean -- all Result Data Assets have an automatically-generated Lineage Graph which shows how the results were created and whether they are reproducible.
Ready-to-use Capsules each of which can be duplicated into your deployment and used with or without customization as an individual Capsule and in Pipelines.
The Code Ocean user interface allows users to connect any number of Data Assets and Capsules in a drag-and-drop interface, while creating a Nextflow script in the background.
You can also import Pipelines from nf-core, a community effort to collect a curated set of analysis pipelines built using Nextflow. It provides portable, documented, automated pipelines that guarantee reproducibility.
A Release Capsule/Pipeline is an end-to-end reproducible and immutable version of your Capsule/Pipeline that is saved in its current state and separate from the original.
Collections are composed of Capsule, Pipelines, No-code Apps, and Data Assets, organized by Administrator-defined topics. They allow for better asset management at the organization level, increased discoverability, and re-use of “Gold Standard” assets.
The Code Ocean API enables users to interact with Code Ocean programmatically, without using the web application and can be used directly or via the Code Ocean Python SDK.
An introduction to the foundational unit used to create, organize, and share projects in Code Ocean. You can learn more in the Capsule Guide .
You can learn more in the Data Assets guide .
You can learn more in the Data Asset Provenance guide .
You can learn more in the Code Ocean Apps guide .
More information about Pipelines, including a full tutorial for building an RNA Seq pipeline .
More information about the Release Process .
You can learn more about creating and using Collections .
is an open-source platform for managing the end-to-end machine learning lifecycle. With Code Ocean's native MLflow integration, you can create MLflow experiments that will track runs from Capsules and Pipelines, monitor and manage your experiments within the integrated MLflow tracking server, and register models for downstream workflows.
Learn more about MLflow and Models in Code Ocean .
More information about the Code Ocean API, including useful examples .
