Bioinformatics

Biology research

French

Roland Santos

Roland Santos
Computer Systems Specialist for IT Operations and High Performance Computing BC Cancer Agency’s Michael Smith Genome Sciences Centre (GSC)

Expertise
Roland is part of the team responsible for the day-to-day operations of the Genome Science Centre’s (GSC) HPC infrastructure. He joined the GSC in 2006, shortly after graduating from the University of British Columbia with a Bachelor’s Degree in Computer Science. He spends every day helping people apply large-scale computing to biological data.

Lindsay Sill

Lindsay Sill
Executive Director, WestGrid

Expertise
As the Executive Director of WestGrid, Lindsay has a deep appreciation for the role of advanced computing in supporting and driving today’s research. She collaborates with leaders in science, technology and innovation from across the country and works to ensure researcher needs at a local level are reflected in Compute Canada’s national activities and strategies. Lindsay joined WestGrid in 2007 and has a Bachelor’s Degree in Biology.

What’s new?
In 2014, the BC Cancer Agency’s Michael Smith Genome Sciences Centre (GSC) – a global leader in genomics and bioinformatics research – became the latest WestGrid and Compute Canada advanced research computing site. This was exciting news for researchers across Canada, giving them increased access to bioinformatics software, expertise and highly secure computing storage. Compute Canada sat down in June 2014 with Roland Santos from the GSC and WestGrid’s Lindsay Sill to discuss what this site will mean for genomics research and health care across Canada.

How does becoming an advanced research computing site compare to GSC’s previous computing capabilities?
Santos:
This includes a scaling up of our operations. The funding from the Canada Foundation for Innovation and the British Columbia Knowledge Development Fund totals nearly $15 million for developing approaches to precision medicine in cancer, with more than half going to fund information technology (IT) infrastructure. This new equipment provides significant robust computing capacity, which will make it possible to process even more data to glean even better insights into genomics and cancer. We will continue to increase our DNA sequencing, data storage, and analysis capacities to handle ongoing research efforts.

What value are we going to see from all this DNA sequencing?
Santos:
DNA sequencing and analysis is part of very promising research in precision medicine, which can be tailored to a person’s specific genetic code. Each case can generate one terabase of data, requiring analysis and storage. To meet the project requirements, we’re currently approaching 10 petabytes of active disk storage, most of it dedicated to storing sequence data. This is enough capacity to store the equivalent of more than 100 years of high-definition video.

Is this DNA sequencing and the analysis done primarily for research purposes?
Santos:
Yes, nearly all of the DNA sequencing data and analysis is for research, primarily on behalf of Canadian researchers and institutions. Increasingly, we’ve been involved in projects in targeted medicines, which make use of our capacity in DNA sequencing and analysis.

Is this infrastructure only available to researchers at the GSC?
Sill:
The GSC will host the equipment but it will be available to the larger Compute Canada user community – any researcher in Canada who has specific bioinformatics or genomics needs. Also, 11 full-time positions will be dedicated to operate the new infrastructure and to help expand the bioinformatics expertise and support across the country. Having that domain-specific technical expertise will be a first for Compute Canada and it will create a stronger and more diverse national platform of computing resources and support services.

Santos:
It also means that researchers at GSC will benefit from access to Compute Canada’s resources, including visualization software and experts, advanced collaboration facilities, and access to national outreach and training activities. This will significantly improve our ability to work together to find better diagnotics and treatments for cancer and other diseases.

Would it have been possible to host this equipment in another province?
Sill:
The specialized legal, security and privacy requirements of health data meant we needed to come up with a customized infrastructure solution. British Columbia was our preferred province because of its leadership in areas of provincial health information and privacy legislation. Within BC, the GSC is well-established as an extremely secure facility with strict access rules and regulations that align with the provincial health privacy policies.

Will this new infrastructure connect to other advanced research computing resources in British Columbia?
Santos:
This new infrastructure will be hosted on-site at the Genome Sciences Centre and is available to researchers as part of our Memorandum of Understanding (MOU) with Compute Canada.

What do you like best about your job?
Sill:
My background is in biology so I know how complex and laborious this research can be. Knowing that we can help save researchers time or improve their ability to tackle large-scale issues — that’s what keeps me passionate about my job.

Santos:
I like knowing that, at the end of the day, I’m doing my part to help researchers and doctors find a cure for cancer.

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