media release

Big data study to benefit biomedicine

August 12, 2013
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Contact:
Cenk Sahinalp, cenk@cs.sfu.ca
Robert Young, 778.782.3351; roberty@sfu.ca
Marianne Meadahl, PAMR, 778.782.3210; Marianne_Meadahl@sfu.ca

Photos: http://at.sfu.ca/GwHwKY

Graduate students aiming to become experts in managing and analysing big data in the area of molecular biology will benefit from a $1.5 million Collaborative Research and Training Experience (CREATE) grant from the Natural Sciences and Engineering Research Council (NSERC).

SFU’s first CREATE grant is being awarded to School of Computing Science professor Cenk Sahinalp. Sahinalp and fellow SFU researchers will collaborate on a six-year project with researchers from the University of Bielefeld in Germany, which is also receiving funding for the project from the German Research Foundation (GRF).

The project aims to address the massive growth of industry data, which often surpasses what computer designers can handle.

The solution has typically been to acquire more computers, establishing bigger clusters, leading systems to become larger and more complex. However, computer scientists are noticing large-scale data does not necessarily need to be processed in conventional ways. Sahinalp suggests that relevant results can still be drawn through data sketches.

“This research focuses on computational genomics and genome sequencing –determining through computer analysis the complete DNA sequence of all the hereditary information contained in an organism at one time,” notes Sahinalp.

The researchers aim to develop a systematic, computational approach to genome sequencing by producing new tools and techniques to address systems, methods and delivery of molecular data analysis.

Genome sequencing may prove to be an important diagnostic tool for certain diseases, such as cancer, he notes. By implementing new methods and algorithms – including algorithms that understand external memory and communication issues – Sahinalp and his team hope to improve how data produced by cancer research is handled and delivered to biomedical scientists.

Approximately 15-20 graduate students are expected to go through the program, which will comprise 10 principal investigators led by Sahinalp. The program aims to produce computer science experts who are knowledgeable about developments in cloud and multicore computing, computer systems technology and new concepts in machine learning.

This is the first CREATE grant to be applied internationally. The two universities are complementary in many ways, with Bielefeld’s project lead, Jens Stoye, and Sahinalp having similar training and research interests.

Other collaborators on the project include members of the Vancouver Prostate Centre and the BC Cancer Agency. 

SFU involvement in second CREATE project

Meanwhile another team of SFU researchers is part of a collaborative CREATE project aimed at providing chemistry graduate students and post-doctoral fellows the opportunity to gain practical medicinal and biological chemistry training in epigenetics.

SFU chemists Robert Young, David Vocadlo and Mario Pinto, V-P Research, are working with researchers from UBC, the University of Montreal, the University of Toronto, Toronto-based Structural Genomics Consortium and international pharmaceutical companies to develop the U of T-led Medicinal Chemistry Network in Epigenetics Training, or ChemNET, a program that includes a two-month intensive practical training program on modern techniques in molecular biology.

ChemNET’s goal is to produce versatile medicinal/biological chemists uniquely suited to anticipate the needs of the evolving chemistry and pharmaceutical sectors in Canada, which will comprise a blend of industrial chemistry, contract research chemistry organizations, small start-up companies and academic drug discovery centres. It will also contribute to open access science by making available the chemical tools developed by its trainees.

Simon Fraser University is Canada's top-ranked comprehensive university and one of the top 50 universities in the world under 50 years old. With campuses in Vancouver, Burnaby and Surrey, B.C., SFU engages actively with the community in its research and teaching, delivers almost 150 programs to more than 30,000 students, and has more than 120,000 alumni in 130 countries.

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Simon Fraser University: Engaging Students. Engaging Research. Engaging Communities.

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