Aus supercomputing facilities join the battle against COVID-19

Tuesday, 21 April, 2020

Aus supercomputing facilities join the battle against COVID-19

Australia’s leading supercomputing facilities, the National Computational Infrastructure (NCI Australia) and the Pawsey Supercomputing Centre have joined the fight against COVID-19 through the provision of streamlined, prioritised and expedited access to computation and data resources.

NCI has announced support for three targeted projects with over 40 million units of compute time, which is equivalent to one single computer doing constant calculations for over 4500 years, on the Gadi supercomputer. NCI will also provide storage for major reference datasets (national or international) needed to support the computational and data analysis by multiple projects.

Meanwhile, the Pawsey Supercomputer Centre has provided access for researchers across five projects to over 1100 cores on the newly deployed Nimbus cloud. Resources being made available at Pawsey include large data stores and the refreshed Nimbus Cloud service. COVID-19 projects will have access to allocations of up to 500 cores, with up to 100 TB of storage available for use during 2020–2021.

“The Australasian Leadership Computing Grants represent a peak merit award for high-performance computing at a scale that is unprecedented within the Australian context, made possible by the federal government NCRIS funding for the new peak facility recently commissioned at NCI,” said NCI Director Professor Sean Smith.

Pawsey Executive Director Mark Stickells added, “Having access to advanced HPC resources and data expertise at Pawsey and NCI allows Australian researchers to accelerate their science to combat the pandemic and we are proud to contribute our national infrastructure and expertise in this collaborative effort.”

The following ALCG-COVID-19 awarded projects will begin computation on NCI’s Gadi:

  • Using large-scale molecular dynamics for rational drug design (The Australian National University) — uses simulations of the around 800,000 atoms that make up a key receptor of the human body to understand exactly how the coronavirus uses it to invade human cells.
  • Structure-based drug discovery (Baker Heart and Diabetes Institute) — aims to model existing or novel drugs, along with drug binding sites, that could be used in treating COVID-19.
  • Targeting structural transitions in the COVID fusion protein (The University of Queensland) — aims to model key structural changes in the protein that enables a coronavirus to enter and infect a human cell, throwing light on a critical target for both vaccine development and the discovery of antiviral agents.

The following projects are already benefiting from Pawsey allocations:

  • Are SARS and SARS-Cov-2 Subclasses of Bat Coronavirus? (The University of Western Australia) — aims to work on a phylogenetic analysis of 75 genomes from SARS-CoV-2, SARS and bat(+civet) CoV to understand the parentage/lineage of those genomes and their similarities.
  • Molecular modelling COVID-19 targets (Monash University) — aims to provide a molecular basis for known antivirals and identify any new ligands which may offer a protective effect.
  • Bayesian Adaptive Trials for COVID-19 Response (Telethon Kids Institute) — aims to develop Bayesian adaptive clinical trials (BATs) for COVID-19 research projects helping to make statistical inference about potential treatment outcomes.
  • Galaxy Australia COVID-19 dedicated Pulsar — provides researchers wanting to rapidly analyse their data with access to a dedicated COVID-19 pulsar via Nimbus cloud resources.

Image caption: NCI’s Gadi supercomputer.

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