April 2, 2020 — With the nation—and the world—disrupted by the COVID-19 pandemic, Pittsburgh Supercomputing Center (PSC) is doing its part in protecting the country’s wellbeing. PSC has been working with a national alliance of high-performance computing resources called the COVID-19 HPC Consortium. As part of this effort, computing time on our Bridges and Bridges-AI platforms is being allotted to urgent COVID-19 computational research. By making these resources available at no cost to scientists, we hope to support the development of new treatments to aid people who have contracted the virus and to limit its spread.
The COVID-19 HPC Consortium encompasses computing capabilities from some of the most powerful and advanced computers in the world. By contributing to this combined effort, we hope to empower researchers around the world to accelerate understanding of the COVID-19 virus and the development of treatments and vaccines to help address infections.
PSC Provides Researchers Access to China’s National Genomics Data Center COVID-19 Database
Working with collaborators at Weill Cornell Medicine, PSC is currently hosting the COVID-19 database for the National Genomics Data Center of the Chinese People’s Republic. By providing ready access to this important dataset, we hope to enable researchers to better understand the COVID-19 virus, helping to control the pandemic in the U.S. and around the world. PSC will host the database on its Bridges platform, which is optimized for the kind of Big Data analysis that will be necessary for the task.
PSC’s Bridges Powers Penn State Effort to Develop Best Practices for COVID-19 Analysis
Thanks in part to PSC resources, the scientific platform Galaxy at the Pennsylvania State University has developed an open source set of computer tools for helping scientists studying the -19 virus obtain transparent and reproducible results.
Galaxy has long been a popular set of tools for scientists studying genetic data and other Big Data research tasks. Galaxy relies in part on PSC’s Bridges platform, automatically routing the largest analysis jobs to Bridges to take advantage of the system’s unique capabilities for managing and computing the most massive data projects.
The purpose of the current open source tools—so named because all the computer code is readily available for scientists to study and critique their programming—is to create a set of standards and rules for handling and calculating using COVID-19 data. Such rules are needed to ensure that a given computation will turn out the same way no matter how many times it is done or which laboratory/computer system carries it out. This, in turn, will help ensure that measures to control or fight the virus will be more reliable and predictable.
For more information on the Galaxy toolkit for COVID-19, see https://covid19.galaxyproject.org/
For more information on Bridges work on COVID-19, see https://www.psc.edu/bridges-for-covid-19-research
The Pittsburgh Supercomputing Center is a joint effort of the Mellon College of Science of Carnegie Mellon University and of the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry, and is a leading partner in XSEDE (Extreme Science and Engineering Discovery Environment), the National Science Foundation cyberinfrastructure program.
Source: Pittsburgh Supercomputing Center