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
Gen3 Community Forum Webinar on Helm Charts
Held Gen3 Community webinar on how to set up Gen3 Data Commons using Helm Chart on various cloud and on-prem platforms. OCC presented Gen3 on GCP using Helm Charts
Publication on Contrived Materials in Liquid Biopsy validation from BLOODPAC
The newest BLOODPAC publication is out. This study sheds new light on how contrived materials—commercially available stand-ins for patient samples—can help streamline the testing and validation of liquid biopsy assays. One step closer to improving outcomes for patients with cancer https://www.sciencedirect.com/science/article/pii/S1525157822003646
Interactive dashboards into the Chicagoland Pandemic Response Commons
Pandemic Response Commons was awarded a grant under AWS Diagnostic Development Initiative, where OCC and AWS team collaboratively worked on the initial implementation of Interactive dashboards into Pandemic response Commons levering AWS Quicksight.
Accelerate research & analysis for Long Covid data
It’s exciting to share that the PRC Long Covid working Group (Northshore, Rush, Sinai, UIC & UChicago) has started submitting the data for research and analysis for Long Covid to the PRC team. This should give us well over 100,000 Long COVID cases to do research and analysis.
OCC team implements Gen3 Workspaces on Google Cloud Platform (GCP).
Open Commons Consortium (OCC) embarked on a project to deploy best practices within their Google Cloud Platform (GCP) tenant. The goal of this project was to deploy a strong foundation that can be built upon with constraints and best practices.
The desired outcome of this project was to develop the GCP foundation setup for Gen3 infrastructure implementation with automation. The scope was also to build up Commons Services Operations Center (CSOC) which will be the master cloud organization for all GCP projects with operational consistency and security with help of Burwood alongside Google. OCC introduced a project based billing for responsible users using cloud computing services.
OCC team publishes paper on Racial/Ethnic Disparities in COVID 19 Case Fatality Rate
OCC team publishes Racial/Ethnic Disparities in the Observed COVID-19 Case Fatality Rate Among the U.S. Population. The purpose of this study was to examine racial/ethnic differences in COVID-19 case fatality rates (CFRs) at the U.S. national level during the first year of the pandemic. We used data from The Atlantic’s COVID Tracking Project (CTP), whose Racial Data Tracker was widely regarded as the most complete source of information on race/ethnicity of COVID-19 cases and deaths during this period.
CFR by month and racial/ethnic group with CTP and CDC datasets
We performed a parallel analysis using the Centers for Disease Control and Prevention (CDC) COVID-19 Case Surveillance Public Use data—an independently compiled and regularly updated individual-level data source. Although less complete than the CTP data, the CDC data contain information on age. Adjusting for age is critical to get an accurate understanding of differences in COVID-19 CFR. We focused on the two largest minority groups, Blacks/African Americans and Latinx, and their comparison to Whites, since these categories are reported most completely by a large number of states and territories, and permit approximate comparability between the two datasets.
AWS Diagnostic Development Initiative awards OCC secondary grant
AWS Diagnostic Development Initiative awards OCC secondary grant to continue the development of The Biomedical Research Hub: a federated platform for patient research data.
OCC team publishes paper on The Biomedical Research Hub
OCC team publishes The Biomedical Research Hub: a federated platform for patient research data. The objective was to develop and operate a cloud-based federated system for managing, analyzing, and sharing patient data for research purposes, while allowing each resource sharing patient data to operate their component based upon their own governance rules. The federated system is called the Biomedical Research Hub (BRH) (https://brh.data-commons.org/).
The BRH is a data ecosystem in the sense that it is a loosely coupled collection of independent data resources that can be explored and analyzed with data portals, workspaces, notebooks, and other applications.