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

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.

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.

OCC team showcases The Chicagoland COVID-19 Commons at SuperCompute 2021 at St Louis, MI.

OCC team demonstrated about how we manage and operate cloud computing and data commons infrastructure to support research.

OCC showcased various services and contributions such as :

  • Our Governance and cloud optimization services

  • How we Build and Manage different Gen3 Data Commons and Data Ecosystems

  • BloodPAC Commons: White House Cancer Moonshot’s goal of sharing data publicly after 5 years using Gen3 Discovery Portal

  • Managing and Reducing cost of Workspaces using Gen3

  • How we contribute to Advancing Scientific Research and Social Impact

AWS awarded OCC with a grant

The AWS Diagnostic Development Initiative will support projects that are using AWS to support research-oriented workloads across four program areas: early disease detection, diagnostics, prognosis, and public health genomics. OCC had applied for a grant to work with the AWS Diagnostic Development Initiative team 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 on their own governance rules.