Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add readme #99

Merged
merged 10 commits into from
Jun 27, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added profile/Gen3_Logo-01_blue.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
55 changes: 55 additions & 0 deletions profile/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
<p align="center">
<img src="Gen3_Logo-01_blue.png" alt="Gen3 logo" width="500" style="display: block; margin: auto; "/>
</p>

# Gen3

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.
michaelfitzo marked this conversation as resolved.
Show resolved Hide resolved

## Gen3 community

### Contributing code to Gen3

Gen3 software is completely open-source. Please refer to our [Contributor Guidelines](https://uc-cdis.github.io/gen3-docs/docs/Contributor%20Guidelines/) for how to contribute code to our repositories.

### Chat with Gen3 staff and the community

If you have questions about operating or using a Gen3 system please contact us. We can be reached on [slack](https://docs.google.com/forms/d/e/1FAIpQLSczyhhOXeCK9FdVtpQpelOHYnRj1EAq1rwwnm9q6cPAe5a7ug/viewform), [discussion board](https://forums.gen3.org/), or via email (support@datacommons.io).

### Events

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](https://gen3.org/community/events/).

### Gen3 releases

Gen3 releases typically happen every month. The lastest release notes can be found [here](https://github.com/uc-cdis/cdis-manifest/blob/master/releases/2024/06/gen3-release-notes.md).

## User Guides

### Setting up and operating a Gen3 data commons or mesh
michaelfitzo marked this conversation as resolved.
Show resolved Hide resolved

Gen3 on [Helm](https://github.com/uc-cdis/gen3-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](https://docs.gen3.org/docs/quickstart).

### Using a Gen3 system

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](https://gen3.org/resources/user/).

## Additional References

### Learn More about Gen3

Check out [gen3.org](https://gen3.org/).

### Learn More about the Center for Translational Data Science

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](https://ctds.uchicago.edu/).