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Q&A: SFU scientist Fiona Brinkman explains the significance of SFU’s new supercomputer, Cedar

April 11, 2017
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By Tia O'Grady

The new SFU Data Centre now has an advanced research computing (ARC) system, or supercomputer, called Cedar. It is one of four new Canadian supercomputing and data centre sites being deployed by Compute Canada, which is renewing Canada’s advanced research computing platform.

Cedar alone has greater computational power than the 50 legacy systems that currently comprise the national platform. So what does this mean for Canadian researchers? What is the significance of Cedar, and why is this a national achievement?

To find out, we interviewed Fiona Brinkman, an SFU professor in molecular biology and biochemistry. In her lab, she undertakes massive computing projects to investigate key infectious disease-causing microbes. Her goal is to understand how they spread and cause illness, and how we might develop more sustainable approaches for controlling them.

Tell us about your research.

Despite medical advances, communicable diseases remain a serious threat to the health and economies of Canadians and people worldwide.

Sequencing the DNA of disease-causing microbes provides accurate data for identifying and tracking infectious disease agents.

The Integrated Rapid Infectious Disease Analysis (IRIDA) Project, led by myself with Will Hsiao (BC Centre for Disease Control) and Gary Van Domselaar (National Microbiology Laboratory), has developed a software platform for more rapidly analyzing and integrating the datasets. Using this software, we can elicit key information about the origins of infectious disease outbreaks, and how to control them.

Overall, IRIDA aims to lead more timely responses to infectious disease threats, whether foodborne, waterborne or airborne, and reduce the impact of infectious disease outbreaks on both public health and economies.

On a more personal level, why is the research important to you?

The IRIDA project addresses a personal goal of mine—to develop new ways to more sustainably interact with the environment and control infectious diseases. The two are related and I have long been interested in studying bacteria as a way of studying the complexity of life. My hope is that through my research I will gain more basic insight into how life is evolving and interacting with various environments, while at the same time very practically developing tools to better control infectious diseases and save lives.

How will Cedar benefit your research specifically?

The software we develop to do these analyses must be housed in a secure environment, with access to adequate storage and computer power. The amount of DNA sequence data that needs to be analyzed worldwide is increasing faster than Moore’s Law (doubling faster than every two years). So we need to come up with more sophisticated ways to analyze the data, coupled with adequately powerful computing resources. As our work expands, our need for more computing resources will increase significantly. Using Cedar and its associated systems, we can meet our goals and be significant players on the international stage in this growing field of genomic epidemiology.

How will the new SFU Data Centre support not only SFU researchers, but other researchers across Canada?

Canadian researchers are already using components of the IRIDA software platform to analyze microbial DNA sequences. The new SFU Data Centre provides key stability in providing these resources, which are securely available online.

Why are Cedar and the SFU Data Centre so important?

Stable access to a secure, powerful computing infrastructure is critical in today’s world. It is even more critical if we are to effectively use microbial DNA as a key tool to better track and control infectious diseases. Thanks to international travel we are increasingly connected globally—and so are disease-causing microbes. Computing resources like this will be increasingly important to more quickly analyze the growing amount of data necessary to track and control disease.