Researchers at the University of Sydney use AWS to accelerate vital genomics research for a range of threatened species

By Amazon Web Services

September 2, 2020

Dr Carolyn Hogg has more than 25 years’ experience in species conservation, inspired by her upbringing visiting South Africa’s Kruger National Park. As Senior Research Manager for the Australasian Wildlife Genomics Group in the Faculty of Science at the University of Sydney, Carolyn’s mission is to help protect rare species, often unique to the country. “Australia separated from the other continents more than 95 million years ago,” she explains. “More than 87% of our mammals, 93% of our reptiles, 94% of our frogs, and 45% of our birds can only be found here in Australia. They are vital for biodiversity and we have a responsibility to ensure their survival.”

For the past decade Carolyn has been focusing on genomics research for the cross-governmental Save the Tasmanian Devil Program. The Tasmanian devil is a rare marsupial, found only on the island state of Tasmania. It is threatened not only due to man-made changes – from extreme climate events like the recent devastating bushfires, to habitat destruction, and vehicle collisions – but also by a contagious cancer that causes facial tumors and has reduced its population by more than 80 per cent.

By using the genome of Tasmanian devils, Carolyn and her team can provide on-the-ground conservation managers with detailed scientific information and insights on how best to protect the species. Their work has accelerated ever since the AWS Cloud trial at the University of Sydney in 2019, enabling them not only to speed up their research, but also to carefully, and more effectively, manage their funding.

Accelerating research

Carolyn says that assembling and annotating genomes – which means identifying the location of specific genes in a genome and determining what they do – used to be a “laborious and resource intensive process.”

“AWS tools and computing power coupled with the RONIN interface – a simple web application that allows anyone to launch complex compute resources – help us to process, analyze, and categorize all of that data, to build the complete picture.”

The University of Sydney, together with RONIN, uses AWS ParallelCluster to create a cluster to run large workloads and sequence the genome of the Tasmanian devil and other endangered species. The team, led by Dr. Carolyn Hogg, was able to complete 18 months of work in six weeks on AWS, and save more than four weeks of queue wait for national supercomputing resources.

Bushfire impact

Now, Carolyn’s team are starting a new project to assemble and annotate the genomes of some of Australia’s most threatened species.

They will be sharing this genome data on the AWS Public Dataset Program, an initiative designed to give researchers anywhere in the world fast, on-demand access to scientifically valuable, publicly available datasets, with the aim of accelerating scientific discovery.

By making the genomic data more easily available to researchers worldwide, they can help to intensify work to protect some of Earth’s most endangered animals in Australia and beyond.

“Australia has the worst mammal extinction rate in the world. We have lost more than 29 species over the past 200 years – that’s 35% of all modern mammal extinctions,” says Carolyn. “The recent Australian bushfires have been catastrophic for our wildlife, pushing even more species to the brink of extinction.”

Democratizing data

According to Carolyn, the only way forward for large-scale genome projects is to “share ideas, data, techniques, and tools”. By democratizing access to data, more people can work with it and get to the answers sooner.

“When you’re dealing with delicately balanced ecosystems, it’s vital to understand the best course of action, based on evidence,” says Carolyn. “When trying to tackle disease, for example, does improving genetic diversity by intervening and moving specific groups of animals improve the situation, or does it actually make the disease more virulent?”

“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.”

“That’s why the AWS Public Dataset Program can be so valuable in so many fields of study. These tools help us to bring the worlds of academia and conservation management closer together than ever before. And when we prove an idea works – it can go global.” The AWS Public Dataset Program covers the cost of storage for some of the world’s most scientifically valuable, publicly available datasets, including those from NASA, the Hubble Space Telescope, the UK Meteorological Office, and the Allen Institute for Brain Science. By making these datasets available in the cloud, the program enables researchers to work with them without needing to download and store their own copies. This allows users to analyze massive amounts of data in minutes, regardless of where they are in the world, or how much local storage space or computing capacity they can access.

Watch this video with a brief interview with Dr Carolyn Hogg, Senior Research Manager for the Australasian Wildlife Genomics Group in the Faculty of Science at the University of Sydney, to learn about the wildlife protection projects using AWS.

Read our blog and learn more about Five ways to use AWS for research (starting right now)

Source: The Amazon blog Day One: How is cloud technology helping to save the Tasmanian devil?

 

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