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Thursday, September 14, 2000

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find related articles. powered by google. Christian Science Monitor Controlling the flood of genetic information
"With the completion of a "rough draft" of the entire human genome in June, government and corporate scientists have assembled enough genetic code to fill 2,000 computer diskettes.

Now, the scientific footrace shifts from spelling out the seemingly endless string of "A's," "C's," "T's," and "G's" that make up our DNA, to actually understanding what it means.

That's where a new field of "bioinformatics" comes in."

"Researchers at the University of Idaho are building their own "super" computer using parts from 40 to 100 desktop PCs. The hardware will cost only about $44,000, but with the proper connections, the system will be sophisticated enough to run experiments on "jumping genes," bits of genetic material that migrate along the DNA double helix like microscopic hitchhikers.

James Foster, the computer scientist at the University of Idaho directing the project, said that building better programs called algorithms is more important to understanding biological data than just building bigger computers.

"Nature can always defeat brute-force approaches," says James Limpan, director of the National Center for Biotechnology Information in Rockville, Md.

"We need the most clever ways of measuring things and not more CPU power," he says."
find related articles. powered by google. Red Herring Blue Gene: a mighty protein prober
"Despite the existence now of a rough draft of the human genome, the story it tells is still full of holes. Just one of them: the mystery of how human proteins get molded into the functional building blocks of life. What's stood in the way of researchers unraveling this puzzle has been the enormous complexity of the chemistry, and inadequate computing power to decipher those intricate workings. That may all change in five years when IBM (NYSE: IBM) researchers enlist the company's newest water-cooled silicon circuits to model the way in which a human protein folds into a specific shape, thus determining its biological function. Called Blue Gene, the supercomputer project will cost $100 million and will be 1,000 times more powerful than Deep Blue, which defeated legendary chess master Garry Kasparov three years ago. It will need all the extra circuitry it can muster, because simulating the behavior of a sinuous strand of protein is no simple task. It involves applying basic principles of physics and chemistry to instruct Blue Gene to calculate the atomic forces at work along a single strand of the human protein. Paul Horn, senior vice president of IBM Research, says this unlocking of protein folding is a milestone in the future of medicine and health care.

Blue Gene is so powerful that even the terminology used to describe its processing abilities is beyond today's computing lexicon. Researchers say it will be able to harness a petaflop of processing power, which is 5 million times faster than a PC. IBM's researchers say the best way to envision that is by imagining a picture one inch tall (representing a single PC processor's capability), while Blue Gene's processing prowess would stretch 30 miles into the sky."

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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