Information technology  

Thousands of computers linked to unravel genetic diseases

9 May 2006

Software developed by researchers at the Technion-Israel Institute of Technology can link thousands of computers to process gene-mapping data tens of times faster than previous programs.

The US National Institutes of Health, Harvard Medical School and scientists in France, Canada, Spain, India and Israel have already utilized the system that uses computers' spare time to unravel genetic diseases. The findings are reported in the June 2006 American Journal of Human Genetics.

Known as Superlink-Online, the system reduces the time-consuming process of identifying the exact location of a disease gene in affected families’ genomes — a crucial step in developing effective disease treatments. “Superlink-Online makes feasible some computations that were not previously possible,” says Dr. Alejandro Schäffer, staff scientist at the National Institutes of Health National Center for Biotechnology Information.

Development started five years ago by Technion Computer Science Professor Dan Geiger and Dr. Ma’ayan Fishelson (at that time Geiger’s doctoral student). Now, with the help of the Condor middleware system, Superlink-Online is running in parallel on 200 computers at the Technion and 3,000 at the University of Wisconsin-Madison. The system can be accessed freely as a password-protected service through the Internet, and final results are combined and output as if they were run on a single computer.

“Over the last half year, dozens of geneticists around the world have used Superlink-Online, and thousands of runs — totaling 70 computer years — have been recorded,” says Professor Assaf Schuster, head of the Technion’s Distributed Systems Laboratory, which developed Superlink-Online’s computational infrastructure.

According to Technion Ph.D. student Mark Silberstein, the system’s current developer, Superlink-Online’s already formidable power (it recently completed in 7 hours computations that would have taken a full year on a single computer) will be increased dramatically in the near future when it is connected to thousands of additional computers using the EGEE computer network, a widespread European network.

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