PROMETHEUS Re-Treat: PDP Launch

We were thrilled to participate in the PROMETHEUS Re-Treat on July 26th in Washington DC, where our Director, Robert Grossman, represented us for the launch of the Prometheus Data Platform (PDP 1.0). This project, led by the Open Commons Consortium, a division of the Center for Computational Science Research Inc (CCSR), in collaboration with our partner, The Center for Translational Data Science at the University of Chicago, marks a significant milestone. Kudos to both teams for their hard work bringing the PDP to life!

PROMETHEUS, which stands for PROject for Military Exposures and Toxin History Evaluation in US Service Members, aims to discover and study advanced precision technologies to prevent, detect early, and enhance treatments for cancers potentially arising from environmental contaminants and toxin hazards faced by military service members and veterans.

Our vision is to integrate federal scientific platforms with public-private innovators to reveal the impact of service-related exposures to environmental contaminants and toxin hazards, and to develop prevention and early detection approaches, as well as advanced treatments for cancers arising from these exposures.

The PDP includes the BLOODPAC Data Commons and the Veterans Precision Oncology Data Commons (VPODC). It also interoperates with the NCI Genomics Data Commons (GDC), Proteomic Data Commons (PDC), and The Cancer Imaging Data Commons (TCIA), all of which have APIs enabling seamless integration with the PDP. These integrations support Apollo data.

The PDP not only provides an environment for PROMETHEUS researchers but also offers a fit-for-purpose governance structure in support of the White House Cancer Moonshot 2.0 data-sharing principles.

Explore the Prometheus Data Platform version 1.0 (PDP) here: PDP 1.0.

This is just the beginning!

Data submission - Perspectives and solutions from different Gen3 systems

Gen3 data submission can be complex and will vary from project to project. The specifics will depend on the data model, data type, use of graph-model and/or metadata service, centrally managed vs user driven, and other project-specific requirements. At this event a range of Gen3 operators showcased on how their projects approach the topic of data submission and how they have managed this process. The event included the following presentations and speakers:

• Data Modelling in Gen3 - Joshua Harris, Research Data Manager, Australian BioCommons

• Data submission into the Aotearoa Genomic Data Repository - Nathalie Giraudon, New Zealand eScience Infrastructure (NeSI)

• COVID-19 Data: 7 Million Records in PRC - Plamen Martinov, Mikisha Patel, Urvi Sheth Open Commons Consortium

• MIDRC: Ingesting Medical Images from Multiple Contributors - Chris Meyer, Center for Translational Data Science, University of Chicago

• g3t: Gen3 Tracker – User Driven Submissions - Liam Beckman, Oregon Health and Science University

The recorded session video is available, providing valuable insights and key takeaways from the event.

OCC and Krumware Teamed Up for Gen3 Implementation Tutorial

OCC collaborated with the Krumware team to demo how to implement Gen3 using Helm charts in AWS from start to finish.

Helm, a tool designed for streamlined installation and management of Kubernetes applications, facilitates the automated deployment, scaling, and management of containerized applications. By leveraging Helm, you'll find the process of creating, configuring, and maintaining your personalized Gen3 Data Commons infrastructure significantly simplified.

Tutorial Highlights

• Introduction to Gen3 Data Commons: Gain an understanding of the Gen3 ecosystem.

• Prerequisites to Configure Helm Charts in AWS: Learn what is needed to get started.

• Step-by-Step Demonstration: Implementing Gen3 using Helm charts in AWS with detailed guidance.

• Setting Up AWS Account and Gen3 Cloud-Automation Locally: Get permissions and set up your local environment.

• Spin Up VPC: Learn to create and configure a Virtual Private Cloud.

• Spin Up EKS: Deploy and manage Kubernetes clusters with Amazon EKS.

• Configuring Helm Charts: Implement Gen3 with precise configurations.

2024 Gen3 Development Roadmap

We had a great Gen3 Community Forum where Director Robert Grossman outlined the Gen3 Data Commons roadmap highlighting key projects. The forum also featured an insightful discussion led by the Gen3 Steering Committee, with Plamen Martinov, Chief Information Technology and Security Officer at OCC, sharing perspectives on features the Gen3 Community is working on and collectively working through a new and improved model for collaboration and co-development. 

The session was a dynamic engagement with the Gen3 Community, and we are enthusiastic about the collective efforts to advance research at the Open Commons Consortium, in partnership with the Center for Translational Data Science, leveraging the robust Gen3 Community.

The recorded session video is available to access, offering valuable insights from the event.

Join Us At Super Compute 2023

We're pleased to announce our attendance at SuperComputing 2023. The Open Commons Consortium will be there with our partner, CTDS, at the University of Chicago to showcase expertise in setting up and managing Gen3 Data Commons and Data Mesh platforms for research. Learn more about OCC services and the latest contributions in advancing scientific research & driving social impact.

Join us at SC2023 and be part of a transformative experience. Stay tuned for more updates, exciting insights, and opportunities to connect with us. See you there! 

Security and Compliance in Gen3 Data Commons

Gen3 facilitates secure and compliant data sharing and analysis for researchers worldwide.

Understanding security and compliance can be a complex subject, which is why we had an event on September 6th in collaboration with our partner, the Center of Translational Data Science at the University of Chicago. This event emphasized security best practices and insights from other Gen3 operators, including the Open Commons Consortium, Krumware, Australian BioCommons, and NeSI, who shared their experiences in setting up and maintaining Gen3 Data Commons and Data Meshes with a security-centric approach.

A brief overview of the topics covered by our esteemed presenters and partners:

1.  A Project Owner’s Perspective on Security & Compliance for Gen3 Data Commons Presented by Robert Grossman, Professor and Director at the Center for Translational Data Science, University of Chicago.

2. Security & Compliance Practices at CTDS Presented by Clint Malson, Director of Security Operations at the Center for Translational Data Science, University of Chicago.

3. Security Practices for Gen3 & Its Applications Presented by Plamen Martinov, Chief Technology Officer of the Open Commons Consortium.

4. Securing Cloud-Native & Kubernetes Environments Presented by Colin Griffin, Founder and Chief Engineer at Krumware.

You can access the recorded session video and PDF slides to catch up on the valuable insights from the event.

OCC team will build up B3 Virtual Biobank Data Commons collaboratively with Rush & Loyola

The Walder foundation Boosters, Breakthroughs, and Biorepositories (B3) grant seeks to exemplify multi-university collaboration and biorepository synergy. As part of the grant, Open Commons Consortium (OCC) is working with Rush and Loyola Medical Center to set up a Virtual Biobank Data Commons. The purpose of the commons is to manage virtual biobank sample metadata between Rush and Loyola Medical Center & this project is led by Jeffrey Schneider. This infrastructure will use Gen3 Platform services, specifically the metadata service (i.e., Discovery Portal).

The initial workstream in 2023-2024 determines the feasibility of operating a stand-alone Data Commons, including a Proof Of Concept prototype using the Chicagoland Region Data Commons Discovery Portal in the Quality Assurance (QA) environment. The secondary workstream in 2024-2025 is to build a standalone Virtual Biobank Data Commons and open it to other investigators either as people seeking samples/collaboration or as partners wishing to merge their biorepository data with the Joint Loyola-Rush Biorepository.

Case study published by Burwood Group : OCC is Democratizing Scientific Research on Google Cloud

The dream held by OCC is to provide the researchers with the data and resources they need to find the answers to the most formidable problems they seek to solve. To make this dream into reality - OCC, Burwood, and Google Cloud accomplished together the result of hard work that made it easy for first time users, students and researchers to access data for continuous research by implementing Gen3 Workspaces on the Google Cloud Platform (GCP). This accelerated the adoption and use of the Gen3 data platform, used by researchers internally to accelerate and democratize the process of scientific discovery, especially over large or complex datasets.

To know more about it, please click here: https://rb.gy/ia1ti

Open Commons Consortium Product Launch

We are delighted to announce the product “Direct Pay" which enables use of pay for compute services for furthering scientific research using a direct payment method on the Gen3  Biomedical Research Hub (BRH).  This is a joint initiative with the University of Chicago, Center for Translational Data Science and AWS Pro Services, DDI initiative to enable the functionality of Direct Pay to BRH, allowing additional payment methods for the use of data mashes and data commons for social impact.

Ten lessons with Data sharing with Data commons

It’s been over a decade that we are working to support and accelerate scientific research by building data commons with the means to share and analyze large data sets in a secure and compliant environment. Director, Robert Grossman discusses lessons learned from this experience & benefits of Data Commons. https://www.nature.com/articles/s41597-023-02029-x