In early April, Australia’s Tier 1 supercomputing facilities, Pawsey Supercomputing Centre (Pawsey) and National Computational Infrastructure (NCI), joined forces to offer additional computation and data resources to support the national and international research community to acquire, process, analyse, store and share data supporting COVID-19 research.
Both facilities contributed extensive resources to assist researchers in the fight to overcome COVID-19. Through this initiative, researchers throughout Australia are now working with NCI which is currently supporting three targeted projects with more than 40 million units of compute time on the Gadi supercomputer; and Pawsey Supercomputer Centre, which provides access across five projects to over 1100 cores on the newly deployed Nimbus cloud.
During this event you will hear updates from ‘hands on’ researchers working on understanding the lineage of the virus, making statistical inference about potential treatment outcomes, COVID-19 targets molecular modelling and more. There will be an opportunity to network with presenters in a relaxed online environment, and a Q&A session will be held at the end of the discussion.
Please feel free to enjoy a drink and snack while joining the presentations.
Please register on the Pawsey website to secure your spot.
PRINCIPAL INVESTIGATOR: Shelley Barfoot - School of Chemistry and Molecular Biosciences at the University of Queensland
Shelley Barfoot received her bachelors in microbiology and computer science through the Advanced Study Program in Science (ASPinS) with honours in computational biology from the University of Queensland. She started as a PhD student in Alan Mark’s group at the School of Chemistry and Molecular Biosciences in 2018. In 2019, she was nominated for a Future Superstars award, and represented the school in the 3 Minute Thesis competition. Shelley is the head tutor of Theory and Practice in Science, one of the foundation mathematics and programming subjects for all first year science students at UQ. Her research primarily focuses on understanding how viruses interact with human cells, a mechanism that is not well understood. When not researching or teaching, she is pursuing a degree in communication, playing Magic the Gathering, or gradually dying her hair every colour of the rainbow.
PROJECT: Targeting structural transitions in the COVID fusion protein
By modelling key structural changes in the protein that enables a coronavirus to enter and infect a human cell, this research project aims to throw light on a critical target for both vaccine development and the discovery of antiviral agents. In particular, working with researchers from one of three centres worldwide charged with rapid vaccine development by the World Health Organisation, the aim is to understand how potential vaccine constructs that incorporate the coronavirus fusion protein can be optimised. Professor Mark and his team will also use the national supercomputer facilities to assist in the global effort to identify existing drugs that could be repurposed to treat COVID-19. The Automated Topology Builder (atb.uq.edu.au), a globally recognised molecular modelling tool developed at The University of Queensland, will be used to develop high quality atomic interaction parameters for all pharmaceutically active compounds that have passed phase 2 clinical trials (efficacy and safety). These will be made freely accessible to researchers at universities and public research institutes worldwide. High quality atomic interaction parameters are needed by researchers trying to identify which currently available drugs might be effective in treating COVID-19 disease. Expanding the number of molecules for which high quality parameters are publicly available will also have long-term benefits in structural biology, computational drug design, materials science and more.
PRINCIPAL INVESTIGATOR: Associate Professor Megan O'Mara - Research School of Chemistry at The Australian National University
Megan studied medical science and worked in pathology labs before returning to university to study physics. Her research uses computer simulations to understand how proteins in the cell membrane act as “molecular machines” to transmit information across the membrane; and how we can design more effective pharmaceutical drugs to treat conditions such as chronic pain, chemotherapy resistance, antibiotic resistance and more recently, Covid-19.
PROJECT: Using large-scale molecular dynamics for rational drug design
This research 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. It is only with high-resolution modelling that accurately replicates the true behaviours of these receptors that we can figure out where vulnerabilities in the virus’ binding process are. Targeting the interaction between the human receptors and the coronavirus binding protein might well be a useful direction for drug design. This project will produce world-first vital information about regions of the receptors that could be potential vaccine or drug targets. Using 48 processors running for 19 days for each of 64 molecular simulations, this research will spend around 13 million units of computing time in the coming months. This amount of high-performance computing is only available on NCI’s new Gadi supercomputer.
PRINCIPAL INVESTIGATOR: Dr Gareth Price is Head of Computational Biology at QCIF Facility for Advanced Bioinformatics.
Gareth manages the diverse spectrum of researcher lead questions involving genomic data, provides training in genomic data analysis, as well as leading the Galaxy Australia (https://usegalaxy.org.au) as Platform Manager. Gareth has 20 years’ experience as a Bioinformatician and Genomics Scientist.
PROJECT: Galaxy Australia COVID-19 Dedicated Pulsar
Galaxy Australia relies on remote (to head node) deployments called Pulsar to increase the range and number of jobs that can be run on the service. The team has been allocated resources on the Nimbus cloud to deploy a dedicated COVID-19 Pulsar as part of Galaxy Australia at the Pawsey Centre that allows Galaxy users to rapidly analyse their data on published tools/workflows to further research into SARS-CoV-2.
PRINCIPAL INVESTIGATOR: Dr Tom Karagiannis Monash University
Tom’s PhD studies were aimed at developing DNA-targeted cancer therapies, these were continued during post-doctoral studies in the Molecular Radiation Biology Laboratory. Tom headed the Epigenomic Medicine Laboratory at the Alfred Medical Research and Education Precinct; Baker Heart and Diabetes Institute and currently at Monash University. In addition, he has been involved in teaching at the Department of Pathology, University of Melbourne.
PROJECT: Molecular modelling COVID-19 targets
The team has been allocated GPU resources on Topaz for COVID-19 targets molecular modelling. In the absence of a vaccine, one of the key immediate research areas is repurposing existing compounds with potential antiviral effects. The research project aims to provide a molecular basis for known antivirals and identify any new ligands which may offer a protective effect.
PRINCIPAL INVESTIGATOR: Associate Professor Michael Wise, The University of Western Australia
Michael is a computer scientist working in computational biology since the early 1990s. His early contributions related to in silico investigations ranging from the plant desiccation tolerance protein LEA to low complexity and natively unfolded proteins. For the last several years he is mostly involved with microbial informatics, and is particularly interested in the evolutionary biology of microbial species, and viruses
PROJECT: SARS, SARS-Cov-2 and MERS are the Same Viral Species, Clades within Bat Beta-Coronaviruses
SARS-CoV-2 and SARS are human coronaviruses of zoonotic origin first transferred from bats to humans in China, regarded as sister clades within the viral species Severe Acute Respiratory Syndrome-Related Coronavirus. A chain of bat beta-coronavirus strains links SARS and SARS-CoV-2. Here I report phylogenetic tree reconstructions in which SARS and SARS-CoV-2 are placed together with related bat strains. We see that single-species models are favoured over speciation models. This is also the case when the phylogenetic trees are computed for MERS and its related beta-coronaviruses in camels, bats and hedgehogs.
Remarkably, single species models still apply even when the datasets are combined across their shared core-proteome. Dated phylogenetic reconstructions suggest that both SARS-like and MERS-like beta-coronaviruses have been circulating for many years, and the population has been largely constant.