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.

UChicago CTDS Gen3 Webinars

Our partners at UChicago CTDS have launched a monthly webinar series to better explain the amazing work they are doing with Gen3. Gen3 is an open source platform for developing data commons. A data commons is a cloud-based software platform for managing, analyzing, harmonizing and sharing large datasets. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets.

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Federal agencies, not-for-profits, and consortiums with members spanning the globe use Gen3 and its framework services to support their research communities, access and index their data, and facilitate scientific discoveries that impact the world.

The next webinar will take place Wednesday, March 13th, 2019 at 1:00pm CDT and will cover technical details of the services that Data Commons Framework created such as Authentication, Authorization and Indexing with Fence & IndexD. Click here to register!

OCC at the 2019 AMS Annual Meeting

We are pleased to announce that Dr. Zac Flamig, Director of Environmental Science, at the Center for Translational Data Science at the University of Chicago and scientific lead for the OCC’s NOAA Big Data Project is participating in the 99th Annual Meeting of the American Meteorological Society (AMS).

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On Wednesday, January 9, he will be sitting on a panel discussion about NOAA’s Big Data Project (BDP). The project is in its fourth year; the panel will be discussing how the project has engaged with the user community and CRADA partners to develop new pathways and applications to serve up NOAA's observations and model outputs through public cloud services.  In this town hall, presenters will provide an update on the progress of the NOAA BDP efforts, including impact on research and applications, lessons learned, and plans for the future

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Open Commons Consortium at SC18

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We're pleased to announce our presence at the 2018 annual Super Computing conference. This year's conference will be in Dallas, Texas. The OCC and the Center for Data Intensive Science are attending and will showcase:

  • innovative applications of data science in biology, medicine, health care, and the environment;

  • new releases of data commons and data peering technology that support research communities, including specialized commons for cancer genomic data, liquid biopsy research, brain disorders, weather data, and satellite imagery;

  • data intensive computing systems;

  • high performance analytics

If you're in Dallas and attending the conference, please stop by booth #3242, ask for a demonstration, and learn more about how we've been making data intensive research easier and more accessible. We'll be giving away OCC first-aid kits, CDIS hot cold packs, and new Gen3 stickers. Get yours while they last!

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