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Australasian Wildlife Genomics Group Cuts Research Time from 10 Days to 5 Hours Using RONIN on AWS

2021

The Australasian Wildlife Genomics Group, a part of the University of Sydney in Australia, studies the molecular genetics and the evolution of gene families and genomes of native Australian wildlife. The group’s researchers focus specifically on wildlife biodiversity and animal extinction threats.

When the group recently started studying reasons for the decline of Australia’s Tasmanian devil population, researchers were limited by the compute capabilities of the university’s on-premises high-performance computing (HPC) environment. “We’ve been studying the population decline for a long time, looking at the disease causing it, and we now use thousands of genomic markers in our research,” says Dr. Carolyn Hogg, senior research manager for the Australasian Wildlife Genomics Group. “Our research was out-stripping our on-premises HPC solution in terms of scalability,” she adds.

As an example, the group’s researchers continually analyze 3.2 billion data points for one Tasmanian devil, a process that sometimes would take up to 10 days to complete because of long wait times for research capacity on the shared HPC queue. As a result, researchers needed more compute capacity and wanted the ability to expand that capacity up or down on demand as they looked at newer data sets.

Dr. Carolyn Hogg releases Bosavi the Tasmanian devil back onto Maria Island after his annual health check
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AWS helps us expand rapidly in real time while we are doing our analysis. Rather than make the data fit the compute we have available, we can make the compute fit the data we have.”

Dr. Carolyn Hogg
Senior Research Manager, Australasian Wildlife Genomics Group

Implementing RONIN and Intel on AWS

To meet its requirements, the Australasian Wildlife Genomics Group decided to move its HPC infrastructure to the cloud, selecting Amazon Web Services (AWS) as its cloud service provider. “The university already used AWS for some compute workloads, and we knew we could gain more flexibility and scalability by using AWS for our research,” Hogg says.
 
The Australasian Wildlife Genomics Group chose to work with RONIN, an AWS Select Consulting Partner, to facilitate the migration. RONIN supplies an HPC environment that relies on Intel-powered Amazon Elastic Compute Cloud (Amazon EC2) C5 instances, which provide faster processing and better scalability than on-premises environments. “The Intel combination of powerful software and processors means we have an answer for anything that comes our way,” says Nathan Albrighton, chief executive officer and founder at RONIN. “We have had great success using AWS and Intel with our cloud-based HPC orchestration engine and platform to help researchers gain the capacity and scalability they need.”
 
RONIN, along with Intel engineers, led a series of workshops and a 13-week proof of concept (POC) to help facilitate the move to AWS. During the POC, RONIN had access to Intel engineering teams to help troubleshoot any issues with the HPC software during the migration.

Reducing Genome Analysis Time from 10 Days to 5 Hours

Running its HPC environment on the RONIN solution, the Australasian Wildlife Genomics Group has accelerated its time to science. “Using RONIN on AWS to run our HPC workloads, we have seen our compute analysis time go from 10 days down to 5 hours,” says Hogg. “This will help us complete our research into the Tasmanian devil population decline faster, and we can use genetic analysis to help our conservation-management partners make more informed decisions around population management.”

Gaining Seemingly Infinite Scalability

The Australasian Wildlife Genomics Group has overcome many of the technical constraints of its HPC workloads and can now scale on demand to support its research needs. “AWS helps us expand rapidly in real time while we are doing our analysis,” says Hogg. “Rather than make the data fit the compute we have available, we can make the compute fit the data we have.”
 
Using the RONIN solution, researchers have seemingly infinite scalability and can seamlessly process genomic data sets of 3 terabytes or more while scaling up or down based on specific research project requirements. “We can scale compute capacity whenever we want, and we have the flexibility to try something for a few days and turn it off again if we need to. This will help us save money going forward.” Hogg says.

Expanding Research Opportunities

Since moving to AWS, the Australasian Wildlife Genomics Group has grown its research opportunities to additional conservation partners. In the future, the group plans to use these HPC capabilities, using the RONIN environment, as a solution for other species. “We’ve now started working on a nationwide threatened species initiative,” says Hogg. “We wouldn’t be able to process these kinds of research data in real-time conservation partnerships without the flexibility and scalability we get from running on AWS.”

To learn more, watch the video below and visit aws.amazon.com/hpc.

University of Sydney’s Wildlife Genomics Group protects wildlife using AWS

About Australasian Wildlife Genomics Group

A part of the University of Sydney in Australia, the Australasian Wildlife Genomics Group studies the molecular genetics and evolution of gene families and genomes of the country’s native wildlife.

Benefits of AWS

  • Reduces genomic analysis time from 10 days to 5 hours
  • Increases scalability for HPC workloads
  • Scales research capacity up or down on demand
  • Expands research opportunities to new departments within the university


AWS Services Used

Amazon Elastic Compute Cloud

Amazon Elastic Compute Cloud (Amazon EC2) is a web service that provides secure, resizable compute capacity in the cloud. It is designed to make web-scale cloud computing easier for developers.

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