HPCwire: HPCVL Resources Used for First Complete Scan of the Human Proteome

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April 09, 2010

HPCVL Resources Used for First Complete Scan of the Human Proteome

Chancellor's Professor of Computer Science F. Dehne building the human proteome

OTTAWA, and KINGSTON, Ontario, April 9 -- Using high performance computing, Dr. F. Dehne and his team of researchers expect to have the entire Homo sapiens proteome complete within a few months.

The proteome is the complete set of proteins produced by a species. Protein-protein interactions are an integral part of many biological processes within the body's cells, including signaling processes to respond to outside stimuli such as the level of oxygen in the environment, transporting nutrients, and responding to threats from viruses such as H1N1 and HIV. Knowing the interactions in cells -- at the molecular level -- is essential for understanding cell behavior. It is also essential for understanding the impact of pathogens on cells.

The Sun Microsystems T5140 cluster located at HPCVL provides the Dehne group with a speedup of close to three orders of magnitude for this task. Without this high performance computing equipment, the first ever complete scan of the human proteome would take well over a year or more rather than just a few months. This would be impossible to achieve without an HPC installation such as HPCVL. The software was optimized to scale up to 6,400 concurrent computational threads, the largest ever calculation of its type ever done at HPCVL and one of the largest performed in Canada.

"HPCVL is pleased to be able to provide world-class computational resources for distinguished scientists such as Dr. Dehne. We are really excited about being able to facilitate this research especially the multi-threaded approach used by this group. Note that as a part of Compute Canada, our resources can be used by researchers across the country," said Dr. Ken Edgecombe, HPCVL's executive director.

"I would like to acknowledge the funding from the Government of Canada, the Canada Foundation for Innovation and the Government of Ontario and thank them for their commitment to ensuring Canadian researchers and scientists have the high performance computing tools and support they need to advance innovation and excellence," said Susan Baldwin, executive director of Compute Canada.

The PIPE software used in this work has been the first to scan the entire proteome of yeast, a key model organism for human cell behavior, and they are currently using HPCVL's resources to scan the entire human cell proteome which is several orders of magnitude larger. PIPE has also been successful in detecting protein interactions between human proteins and pathogen proteins such as HIV. This knowledge will be essential for understanding human cell behavior and helpful for understanding the impact of certain disease-causing viruses such as HIV. The PIPE software was developed by a team of Carleton researchers: Prof. Frank Dehne of Computer Science; Prof. Ashkan Golshani of Biology; Prof. James Green of Engineering; Dr. Sylvain Pitre, Andrew Schoenrock and Chris North of Computer Science; and Mohsen Hooshyar of Biology.

HPCVL is a part of the Compute Canada National High Performance Computing platform and one of Canada's leading secure HPC environments. It has been designed, built, and is run in a secure virtual manner. It is accessible from anywhere in Canada providing researchers with the secure HPC resources they need to do innovative research that will help build Canada's economy while providing high return on capital investment for government and industry.

About HPCVL

HPCVL is comprised of Queen's University, The Royal Military College of Canada (RMC), the University of Ottawa, Carleton University, Ryerson University, Seneca College, Loyalist College and St. Lawrence College. In addition to reliable, secure computing, HPCVL provides storage resources and support for over 130 Canadian research groups and over 800 researchers, and is one of Canada's leading secure HPC environments. Public funding is provided by the Ontario Ministry of Research and Innovation, the Ontario Research Fund (ORF), the Canada Foundation for Innovation (CFI), the Ontario Innovation Trust (OIT), and the federal Natural Sciences and Engineering Research Council (NSERC). For more information about HPCVL, visit www.hpcvl.org.

About Compute Canada

Compute Canada is leading the creation of a powerful national HPC platform for research. This national platform integrates high performance computing (HPC) resources at seven partner consortia across the country to create a dynamic computational resource. Compute Canada integrates high-performance computers, data resources and tools, and academic research facilities around the country. These integrated resources represent close to a petaflop of computing capability and online and long term storage with rapid access and retrieval over Canada's national, provincial and territorial high-performance networks. www.computecanada.org.

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Source: HPCVL

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