The University of Chicago, Center for Translational Data Science is the maintainer organization for the open-source Gen3 Data Platform. Some useful references are included below to help you learn more about Gen3.
Gen3 software is completely open-source. Please refer to our Contributor Guidelines for how to contribute code to our repositories.
If you have questions about operating or using a Gen3 system please contact us. We can be reached on slack, discussion board, or via email (support@gen3.org).
We hold regular forums on a variety of topics to engage with and hear from the community. You can find previous and upcoming events here.
Gen3 releases typically happen every month. The lastest release notes can be found here.
Gen3 on Helm is the new preferred way to deploy a Gen3 commons or mesh. Using Helm, a package manager for Kubernetes, Gen3 can be installed against any cluster, including a local one such as Minikube or Rancher Desktop. Helm is a tool that streamlines the installation and management of applications on Kubernetes platforms. Helm plays a crucial role in simplifying the deployment and management of Gen3 components within your environment.
This option is suitable for all deployments. If you are ready to get started, you can follow our guide here.
To learn more about interacting with a Gen3 data commons or mesh including how to create a data dictionary, upload data and metadata, indexing files, and other topics please refer to our user guide found here.
Check out gen3.org.
The Center for Translational Data Science at the University of Chicago is developing the discipline of data science and its applications to problems in biology, medicine, healthcare and the environment. We develop and operate large scale data platforms to support research in topics of societal interest including cancer, cardiovascular disease, inflammatory bowel disease (IBD), birth defects, veterans’ health, pain management, opioid use disorder, and environmental science. We also develop new machine learning and AI algorithms over the data in our platforms.
Our center has been at the forefront of data sharing by continuously leveraging new approaches and new technology to enable world class science in a variety of fields. We have developed a number of important firsts: including one of the first large scale data clouds (NSF supported Open Science Data Cloud (2010-2016)), the first data cloud designed to host biomedical data and approved as a NIH Trusted Partner (Bionimbus Protected Data Cloud (2013-present)), the first large scale data commons (National Cancer Institute’s Genomic Data Commons (2016-present)), and the first set of services to create data ecosystems or meshes for biomedical data (Data Commons Frameworks Services for the Cancer Research Data Commons (2020-present)).
Today with our partners, we operate a data ecosystem comprising over 20 data commons that make over 17 PB of data available to the research community from nearly 1.7M patients. We provide access to this data via secure and compliant workspaces, while protecting patient privacy. These are all based on the open-source Gen3 data platform, that includes the Gen3 data commons, Gen3 Framework Services, and Gen3 Workspaces.
We are based in Chicago, but our work engages collaborators from across the world.
You can find out more here.
