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November 5, 2010

"Beagle" supercomputer nears completion

The University’s Beagle Super Computer, a supercomputer dedicated to biomedical research, is slated to finish construction mid-December and to start retrieving data in February.

The Beagle is part of a joint venture between the University and Argonne Labs that has been funded by a grant from the National Institute of Health.

“A supercomputer is a way of answering questions that you couldn’t otherwise answer,” said Ian Foster, director of the Computation Institute and principal project investigator. “It’s like an accelerator of human ingenuity.”

At 150 teraflops, and 18,000-core Cray XE-6 supercomputer, the Beagle will be the largest computer in the world dedicated to biomedical research.

“It’s going to be very integrated with the University’s biomedical infrastructure,” Foster said. “The most exciting part about it is the people doing really interesting research.”

The computer is named after the HMS Beagle, the ship Charles Darwin used to sail around the world and conduct his Galapagos Islands research. The computer will be ready to begin computing February 12, the 202nd anniversary of Darwin’s birth, according to a press release.

A number of teams will use the Beagle for biomedical research, including biochemistry and biophysics professor Benoit Roux.

“Mostly what we do is computational studies on membranes and proteins,” Roux said. “We use molecular dynamic simulations. So that requires simulating the movements of the atoms by the function of movement over time.”

Roux will work on exploring ion channels by using the Beagle.

“We’re working on understanding how proteins are able to decide that this is the correct ion because ions are very similar,” Roux said. “To understand that you need to do very detailed calculations.”

The consequences of the information that can be gleaned from the ion channel research could be widely useful, Roux said.

“This has applications for a wide variety of diseases,” Foster said. “If we can work out how these ion channels look in normal people and diseased people, we can start trying to figure out how to treat them.”

Roux’s work will be some of the first to use the Beagle when it goes online in December. But he doesn’t expect it to go perfectly on its first run.

“Typically a big computer like that you have some problems, so they like to sort of drive it around the block first,” Roux said.

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