Building supercomputing into bioinformatics
As Pawsey’s first bioinformatics platforms specialist, Audrey Stott is attuned to what biologists need to support their research, and how to help them get it. With an established background in human biology, podiatry and clinical research, Audrey moved into biomedical research by completing a Masters degree in biomedical science. This exposed her to supercomputing for biological analyses, particularly bioinformatics and data analysis for genomics research, and subsequently became a turning point for her career.
Audrey now builds, optimises and deploys containers for bioinformatics, deploys specialist bioinformatics software on High Performance Computing (HPC) and the cloud, develops instructions for using HPC, and collaborates with researchers needing larger and faster data processing. “I assist researchers in installing the software they need, getting workflows written and running, and help them make full use of the resources they require,” Audrey says.
Helping biologists process their research data in the best and most efficient way possible means that Audrey works with experts across Pawsey. “There’s fairly constant two-way communication with the help desk staff and the infrastructure and system administrators to build on their expertise in hardware information and software deployment,” she elaborates. “I also work with the education and training team to develop training material, documentation, webinars and workshops for researchers wanting to use Pawsey resources. Our bioinformatics team works across every aspect of raising awareness with biologists and making it easier for them to use HPC in their research.”
“The easier and faster it is for them to process their data, the more time they can spend on experimentation and writing, and the sooner they can get their research out to where it can make a difference.”
Audrey considers the relationships with her colleagues maintaining strong research communities of Pawsey users as one of the best parts of her job. “There’s a great work culture here, everyone is very supportive and cohesive, and we are all about looking outwards and helping the researchers. It’s really exciting to be building supportive and dedicated expertise for the bioinformatics and biology domains, and collaborating with both the research and HPC communities to optimise HPC resources for their needs.”
Job satisfaction comes from helping more bioinformatics users feel more equipped and confident in approaching and using HPC. And although Audrey has been with Pawsey for less than a year, her ambitions for the future continue to grow. “Just like we’re doing for bioinformatics, I’d love to get to the point where every scientific domain is supported at Pawsey by a dedicated team with a structured way to use the infrastructure and resources that suits the specific research needs. Every researcher in Australia should be able to confidently sign up to use HPC to upscale their research.”