Murdoch University Case Study
Murdoch University, founded in 1973 in Western Australia, is a public research university with more than 16,000 students. Located in Perth, with additional campuses in Singapore and Dubai, Murdoch is ranked in the top 500 universities in the world and is a member of Innovative Research Universities Australia.
Our time-to-science is definitely faster using AWS. We’re spending more time solving the genomic problems we need to solve, because we don’t have to worry about data center maintenance or management."
Associate Director, Centre for Comparative Genomics, Murdoch University
Researchers at the University’s Centre for Comparative Genomics (CCG) had a major challenge on their hands—how to quickly and effectively sequence the genome of the cattle tick. The cattle tick, a parasite of cattle, causes billions of dollars of annual economic losses to cattle producers throughout the world. In northern Australia, cattle ticks can spread fever and other diseases that are responsible for a US$146 million annual loss for the country’s cattle industry. “We want to help the industry develop an effective tick vaccine, and the best way to do that is to sequence the genome,” says Professor Matthew Bellgard, director of the CCG. “Sequencing the genome quickly, though, is a massive and complex bioinformatics undertaking, because the cattle tick genome is over two times the size of the human genome. We are working very closely with our colleagues at the United States Department of Agriculture, led by Dr. Felix Guerrero, Project Leader of the US Livestock Insects Research Laboratory, based in Kerrville, Texas.”
Initially, the CCG conducted cattle-tick genome analysis using supercomputers at publicly funded academic research providers. However, researchers became frustrated by the supercomputers’ performance and reliability characteristics. “Supercomputers are technically challenging to operate, especially when they are being utilized by multiple scientific domains with competing computational requirements. As a result, they can experience periods of service disruption or degraded performance. This translates to a significant amount of research time lost, as analysis processing can take weeks,” Bellgard says. In addition, CCG researchers needed to conduct analysis in a more agile way, rather than relying on the more rigid usage patterns of the academic environment.
As a result of these challenges, CCG did not have full control over the scientific process. “Our progress on cattle-tick genome research was being hindered,” says Adam Hunter, associate director of the CCG. “We wanted to get the research done faster and easier.”
Why Amazon Web Services
The CCG decided to move its research to the cloud as a way to solve its challenges. “We knew investing in a public cloud solution would help us mitigate a lot of the risks we were dealing with,” Hunter says. The Centre chose Amazon Web Services (AWS) as its cloud platform for genomic sequencing. “Choosing a public cloud was a no-brainer for us,” Professor Bellgard explains. “AWS is an established player in cloud technologies, and it offers a compelling combination of functionality, performance, and availability.”
The CCG moved its cattle-tick genome research project to the AWS Cloud, using Amazon Elastic Compute Cloud (Amazon EC2) instances and Amazon Simple Storage Service (Amazon S3) for genomic data storage. CCG uses the Amazon Glacier storage service for long-term storage of raw genomic data sets.
The CCG also uses AWS CloudFormation templates to assist with architecture design and reproducibility, and Amazon Simple Queue Service (Amazon SQS) to provide message scheduling. Additionally, the Centre uses Amazon EC2 Spot Instances to purchase discounted Amazon EC2 capacity through a bidding process. “We are starting to save a lot of money by using EC2 Spot Instances,” says Hunter.
Researchers at CCG are now able to achieve results faster than before. “Our time-to-science is definitely faster using AWS,” Hunter says. “We’re spending more time solving the genomic problems we need to solve, because we don’t have to worry about data center maintenance or management. There are fewer barriers to our research now.”
Using AWS, the CCG was able to easily facilitate an international consortium of researchers who are developing cattle-tick vaccines. “Because our AWS Cloud environment enables us to be more productive, the consortium is helping cattle ranchers fight the cattle-tick problem in the Americas, Africa, and Australia,” says Bellgard. “Moving to AWS eliminated delays and helped us complete our research project months faster.” By analyzing data at a faster speed, consortium researchers were able to more quickly identify novel tick proteins that will serve as active ingredients in next-generation anti-tick vaccines for cattle. Also, three international animal health companies have entered into official cooperative research agreements to bring discoveries from the CCG cattle-tick genome project to the field.
CCG can also be more agile in its approach to performing genomic research. “Using the cloud, we have full control over our research, so we are better able to mitigate external risks,” says Bellgard. “We are no longer limited by the resource allocation process for academic supercomputers or even by the ability to implement software. We can control everything using AWS, which means we can more easily customize our platform to suit specific workloads.”
While it continues to perform cattle-tick genome research in the cloud, the CCG has also moved its core workloads to AWS. “This has been transformative, removed technical barriers, opened new opportunities, and allowed us to mitigate risk associated with legacy approaches to infrastructure,” says Bellgard.
About Murdoch University
Murdoch University, founded in 1973 in Western Australia, is a public research university with more than 16,000 students
AWS Services Used
Amazon Simple Storage Service (Amazon S3) is an object storage service that offers industry-leading scalability, data availability, security, and performance.
Amazon Elastic Compute Cloud (Amazon EC2) is a web service that provides secure, resizable compute capacity in the cloud.
Amazon S3 Glacier
Amazon S3 Glacier and S3 Glacier Deep Archive are a secure, durable, and extremely low-cost Amazon S3 cloud storage classes for data archiving and long-term backup.
AWS CloudFormation provides a common language for you to describe and provision all the infrastructure resources in your cloud environment.
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