Computing Science

NSERC Create grant combines big data and biology

August 12, 2013

Computing Science professor Cenk Sahinalp is the first SFU recipient of NSERC’s Collaborative Research and Training Experience (CREATE) grant. Sahinalp and fellow SFU researchers will work together with the University of Bielefeld in Germany, comprising nearly 20 collaborators who will be granted $1.5 million in NSERC funding over six years. The University of Bielefeld has also been approved for substantial funding from the German Research Foundation (DFG) for the program.

The project will provide training for graduate students aiming to become experts in big data management and analysis in biological sciences, in particular biomolecular data. Data is growing on a massive scale in many industries, often surpassing the ability of computer designers to handle its growth. In the past, the solution was 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.

Sahinalp’s 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. Through the CREATE program, he and his colleagues aim to develop a systematic, computationally sound 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. By implementing new methods and algorithms – including algorithms that understand external memory and communication issues – Sahinalp and his team hopes to improve how data produced by cancer research is handled and delivered to biomedical scientists.

Approximately 15-20 Masters and PhD students are anticipated to participate in the Computational Methods for the Analysis of the Dynamics and Diversity of Genomes (MADD-GEN) program, which will comprise 10 principal investigators, with Sahinalp the overall lead. 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.

The University of Bielefeld was first to receive the program announcement, and subsequently reached out to SFU to initiate a partnership. The two universities are complementary in many ways, with Bielefeld’s project lead, Jens Stoye, and Sahinalp having similar training and research interests. This is the first CREATE program to be done internationally, in conjunction with another university. Other collaborators on the project include members of the Vancouver Prostate Centre and the BC Cancer Agency.