Supercomputer to speed up genomic sequencing

Gregor Heard
By Gregor Heard
Updated November 20 2020 - 1:37am, first published 12:00am
Philipp Bayer, University of Western Australia Forrest Fellow and bioinformatics researchers, says a new supercomputer cluster will be a boon for agricultural researchers.

AGRICULTURAL researchers will be among the beneficiaries of an upgrade at the Pawsey Supercomputing Centre in Perth.

The centre is a joint venture between CSIRO, Curtin University, Edith Cowan University, Murdoch University and The University of Western Australia, supported by the Western Australian and Federal Governments.

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Pawsey recently announced the purchase of a new supercomputer, in the centre's biggest upgrade since opening in 2009, funded by a government grant.

The new supercomputer will deliver up to 50 petaFLOPs, or 30 times more compute power than its predecessor.

While the technicalities are better appreciated by tech boffins, the upshot for the agricultural community is better and faster genomic sequencing, critical in breeding new varieties.

But the computer's benefit to agriculture does not stop there.

It will also be utilised to develop AI-enabled ways to help farmers reduce herbicide use.

The new supercomputer is part of Pawsey's Capital Refresh Program, delivered under a $70 million grant from the Australian Government in 2018 to upgrade its supercomputing infrastructure.

Philipp Bayer, bioinformatics researcher at the University of Western Australia, said the supercomputer would be a massive time-saver when sequencing.

"What used to take up to six months will now be possible in four weeks," Dr Bayer said.

He said he saw the biggest possibilities in the canola and wheat spaces.

"Wheat has a massive genome so it is a time-consuming affair," he said.

He said the technology would allow researchers to look at novel germplasm from gene banks, such as wild relatives, for useful material such as drought or disease tolerance.

"We can look at genes and alleles and see if there is anything useful there," he said.

He said the processing power of the supercomputer, which can handle 800 graphic processing units (GPU) helped with the data-dense work, compared to 64GPU previously.

There are also massive energy savings.

"The unit uses 25 times less power than the previous cluster," Dr Bayer said.

He said the major benefit would be making this kind of technology relatively accessible to ag researchers.

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"It is still expensive but this makes it much more accessible," Dr Bayer said.

Gregor Heard

Gregor Heard

National Grains Industry Reporter

Gregor Heard is Fairfax Ag Media's national grains industry reporter, based in Horsham, Victoria. He has a wealth of knowledge surrounding the cropping sector through his ten years in the role. Prior to that he was with the Fairfax network as a reporter with Stock & Land. Some of the major issues he has reported on during his time with the company include the deregulation of the export wheat market, the introduction of genetically modified crops and the fight to protect growers better from grain trader insolvencies. Still involved with the family farm he is passionate about rural Australia and its people and hopes to use his role to act as an advocate for those involved in the grain sector. Away from work, he is a keen traveller, having spent his long service leave last year in Spain learning the language.

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