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Gene genie almost out of bottle

The time is nigh for IBM's Blue Gene project

One of IBM's key researchers was in Australia this week to tout the progress of the company's £70m Blue Gene project.

And the news, according to Dr Ajay Royyuru, the manager of structural biology with IBM's Computational Biology Center, is that the launch of the world's most powerful supercomputer is a step closer as Blue Gene moves into the production stage.

In Melbourne for the recent 'Beyond The Human Genome' conference, held by the Commonwealth Scientific and Industrial Research Organisation, Royyuru said IBM was also tackling the problem of how to keep a machine capable of more than one quadrillion (1,000,000,000,000,000) operations each second busy.

"Think of a traffic cop at a four-way intersection using hand signals to control traffic, then change that to a 400-way intersection but still only one cop. You have to figure out a different way of moving all that traffic," he said. "So we have to scientifically decompose the problem to keep the machine busy."

He said IBM had formed several science and industry alliances with groups around the world, including Australia, to gain input on the types of problems Blue Gene could be used to tackle.

He also said the company would run its second Blue Gene Protein Science Workshop in Edinburgh, Australia in March to develop possible applications with protein scientists from around the globe.

Royyuru said the problem of understanding protein folding was akin to being given 10 foreign language books but no dictionary.

"The genome is giving you a sort of parts list, but we don't know how to put these parts together, what they are doing in the cell or how they are contributing to life," he said. "We need to observe the shape and structure of the proteins produced by genes because the function of every protein is predicted by that shape and structure."

Royyuru said current methods using experimental structure determination cost time and money and did not always provide adequate answers.

"We can [currently] watch about a microsecond in [real] time of protein folding, but as most proteins take milliseconds to seconds to fold, we are about 1000 times short of being able to simulate this," he said. "Also, a single simulation doesn't tell you anything in science — you need to watch hundreds to thousands of simulation trajectories to derive answers. Blue Gene is a step in that direction."

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