The University of Sydney is using cloud computing and data sharing to accelerate genomics research into endangered species, including the Tasmanian Devil.
In a partnership with American public cloud giant Amazon Web Services announced this week, the university is expanding its genome research and making data available through the AWS Public Dataset Program, an initiative where scientists share research and huge datasets.
Australia has the worst rate of mammal extinction in the world, losing more than 29 species over the last 200 years – 35 per cent of all modern mammal extinctions.
Australian researchers believe they can reduce that rate by better understanding the genomes of some of Australia’s most threatened species.
Dr Carolyn Hogg, a Sydney University researcher with 25 years’ experience in animal conservation says assembling and annotating animal genomes has traditionally been a manual and laborious task.
“Imagine I gave you a 5,000-piece jigsaw, but I didn’t give you the picture to work from. How do you solve it? Firstly, you spread all the pieces out – taking up a huge amount of room – then you find the edges. Slowly you start to slot bits together and you contract the space used by the other pieces.
“We’re often working with more than a billion pieces of jigsaw and no guide.”
By using AWS cloud computing and a simple web application, Hogg says her team can access sophisticated compute resources, which helps to process, analyse and categorise the genome data – “to build the complete picture.”
For example, a better understanding of the Tasmanian Devil’s genomes helps Hogg arm conservation managers with better intelligence on threats to the mammal such as the rare form of cancer that has ravaged the species.
“The types of issues Tasmanian devils face are often very similar to those faced by other threatened species, such as the koala, orange-bellied parrot, or the woylie – an extremely rare, small marsupial.
“These range from low genetic diversity, to a high rate of infectious disease, and a fragmented landscape. As the devil population drops, genetic diversity also decreases. This leads to inbreeding, weaker immune systems, and a vicious cycle of more disease.”
“In turn, that has serious knock-on effects for other wildlife in the area, because the devils are at the top of the food chain.”
The University of Sydney has been trialling using AWS technology for genome research since last year. It will be expanded further, the university says, and the research will be widely shared.
Hogg says sharing these types of data and research methods is vital for saving other species, including those outside Australia.
“Even with fragmented information, you can start to establish patterns. And often these patterns are true in other species. They can be used to draw certain conclusions or rule out other ideas.
“In terms of scaling this up to benefit other species, the ultimate goal would be to create a universal genomic library and tools that other researchers and conservation managers can access in order to make science-based decisions.”
The AWS Public Dataset Program is one popular method for sharing research. Used by organisations like NASA, the Hubble Space Telescope, the UK Meteorological Office, and the Allen Institute for Brain Science, Hogg says it can connect academia and conservationists in new ways.
“And when we prove an idea works – it can go global,” Hogg says.
The Amazon program already hosts two of the world’s largest cancer genome sets and other endangered species. The data is hosted on the AWS platform meaning researchers accessing it do not need to download entire datasets to run an analysis.
Iain Rouse, AWS country director for public sector in Australia and New Zealand said the University of Sydney project is a great example of how cloud technology can accelerate research outcomes.
“AWS’s tools and computing power, combined with APN Partner RONIN, allows anyone to utilise a simple web application to launch complex compute resources,” Rouse said.
“This combination of technologies helps the university to process, analyse, and categorise its data to build insights and in doing so, help solve some of the biggest community and environmental issues in the world.”