Volume 12, Number 4 October 8, 2004

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Bioinformatics computer cluster again helps ‘virtual supercomputer’

By Colleen MacPherson

Once again, a U of S computer cluster was called into service as part of a virtual supercomputer project, this time to trace the motion of tens of thousands of atoms in an effort to figure out how proteins fold.

According to Computer Science Prof. Tony Kusalik, this is the third time the U of S has been involved in a Canadian Internetworked Scientific Supercomputer (CISS) project. Lasting 48 hours in mid-September, CISS-3 tackled a job from researchers at the Universities of Calgary and Toronto and, at one point, there were 3,547 concurrent jobs running on some 4,000 computers in 27 locations across the country.

The problem, described as the “Holy Grail” of modern biology, was understanding how proteins fold. Proper folding is essential to a protein’s function while misfolding can lead to disorders like Alzheimer’s and “mad cow” disease. The results are expected to have applications in biotechnology, basic biomedical research and pharmaceutical science.

Kusalik said he has not heard the outcome of the project but “in cases like this, no news is usually good news”.

The computer cluster used in CISS-3 is in the Bioinformatics and Computational Biology Research Laboratory, and is one of about a half-dozen clusters on campus. By combining many clusters, researchers can access the kind of computing that is beyond the capabilities of one research group or institution.

In a previous project, in November 2002, the CISS set a Canadian benchmark by completing 3.5 years’ work of computation in a single day.

Participating in projects like the CISS is not only enhances the University’s reputation, but is a requirement, said Kusalik. In funding the purchase of computer clusters, the Canadian Foundation for Innovation (CFI) requires that 20 per cent of operating time is set aside for outside users.

In addition to virtual supercomputer projects, there are a number of efforts underway in Canada to set up grid computers. These, explained Kusalik, use the free time on linked computers to work on jobs fed into the grid by participants. An example of an existing grid computer is the SETI@home project which uses down time of home computers to search for extraterrestrial intelligence.

So far, U of S researchers have not made use of the CISS, but “that would be great if they did”.

For more information, contact communications.office@usask.ca

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