Gen3 - User Guide

Welcome to the Generic Gen3 Data Commons Documentation


The Center for Data Intensive Science (CDIS) at the University of Chicago has developed and maintains the Gen3 software stack to help accelerate scientific discovery through creation of a collaborative infrastructure that enables sharing of information between stakeholders in industry, academia, and regulatory agencies.

The Gen3 software stack is a collection of microservices that enable the standing-up of data commons, which allows different partner organizations to pool data and grants approved researchers access to harmonized datasets in a scalable, reproducible, and secure manner.

This documentation describes the commons and provides a user guide to assist data contributors and analysts.

Guiding Principles


We believe that data must be open and accessible within the research community to collectively achieve the critical mass of data necessary to power data-driven research, insight, and discovery.


We believe that collaboration creates a knowledge pool that not only drives better software development, but also connects us to a active community in pursuit of shared social impact. We have long benefitted from open-source software and are committed to contributing to future generations of software and scholars.


We believe that rapid innovation is most effectively achieved through an open infrastructure environment where portability and compatibility are maximized and knowledge is distributed broadly.

For more information visit: CDIS Guiding Principles


Operation of the Gen3 commons is supported by generous grants from Amazon Web Services’ Grants for Research Credit Program and Microsoft Azure’s Research Grant Program.

The Data Commons Architecture

User access to the Gen3 data commons runs through a VPC or Virtual Private Cloud. Access to data and analysis tools through a Virtual Private Cloud (VPC) allows for balance of usability and security. All access is through a monitored head node. Data is not directly accessed from the Internet.

Other secure and compliant Gen3 member systems (including cloud based systems) can access Gen3 data through the API.

Diagram of the System Architecture

Gen3 Architecture

Contact CDIS Staff