Blue Gene

John Clark (
Tue, 7 Dec 1999 12:20:07 -0500

12/06 11:08 FOCUS-IBM supercomputer "Blue Gene" to probe gene mysteries

By Eric Auchard

NEW YORK, Dec 6 (Reuters) - International Business Machines Corp. <IBM.N> on Monday said it plans to spend $100 million to build a supercomputer far faster than any existing machine and put it to work pushing the boundaries of what is known about how proteins are formed and their role in human disease.

The ambitious plan envisions a new RS/6000 computer, named "Blue Gene," capable of more than 1 quadrillion operations per second, or 1,000 times more powerful than the Deep Blue machine that beat world chess champion Garry Kasparov in 1997.

IBM said the new supercomputer system, which will take up to five years to construct, will initially be used to model how proteins fold, thereby giving scientists and doctors better insight into diseases and ways to combat them.

Projected to be 500 times more powerful than any current computer, Blue Gene would help pharmaceutical companies design prescription drugs customized to the needs of individual people. It would also allow doctors to respond rapidly to changes in bacteria that lead to drug-resistant viruses.

IBM's breakthrough technology undertaking would build on the roadmap being created by the Human Genome Project, a public and private industry initiative that has set a goal of deciphering the entire human genetic code by 2005.

"Breakthroughs in computers and information technology are now creating new frontiers in biology," said Paul Horn, senior vice
president of IBM's research division.

In a phone interview, Horn painted a vision of how the IBM project would allow patients to one day walk into a doctor's office and have a computer analyze a tissue sample, identify any ailment, and then instantly prescribe a treatment suited to specific illnesses and the individual's genetic makeup.

IBM's Blue Gene will consist of more than 1 million processors, each capable of 1 billion operations per second, the Armonk, N.Y.-based company said. That would make it 2 million times more powerful than today's personal computers.

The research project initially would entail folding a 50 amino-acid sequence, Horn said. Once the Blue Gene computer system is fully installed in four to five years, IBM envisions being able to fold 300 to 600 sequences, a research project that would alone take up to one year to complete, he said.

Proteins, which control all cellular function in the human body, fold into highly complex, three-dimensional shapes that determine their function. A change in the shape of a protein can dramatically change its function, and even a slight change in folding can turn a desirable protein into a disease.

Blue Gene is the latest "grand challenge" undertaken by IBM to push the limits of computing power to solve fundamental research problems viewed by the scientific community as having the potential to change the world, or at least the way we think about the world.

In a similar daunting research challenge a decade ago, IBM researchers created a computer capable of simulating the Grand Unified Theory of quantum electrodynamics, what physicists see as the standard theory of the forces of nature.

"We think a tremendous gain in performance will be made possible by the first major revolution in how computers are built since the
mid-1980s," Ambuj Goyal, vice president of computer science at IBM's research unit, said in a statement.

Horn said the radical new design will represent the biggest change in computer architecture since the development of faster and simpler Reduced Instruction Set Computing (RISC) replaced Complex Instruction Set Computing (CISC) in the 1980's.

The new design has been nicknamed SMASH, which stands for "Simple, Many and Self-Healing," and which will create a self-stabilizing computer that can automatically overcome the failure of individual components.

The SMASH architecture also differs from existing computers in that it further simplifies the number of instructions carried out by each computer chip, allowing them to work faster.

SMASH will allow a massively parallel processing system capable of handling more than 8 million simultaneous threads of computation, compared with a current maximum of 5000 threads.

Blue Gene's more than 1 million processors will be housed in a massive room-sized machine composed of 64 six-foot-high racks of computer chips taking up nearly 2000 square feet of floor space.

The computer maker said about 50 scientists from its research group's Deep Computing Institute and Computational Biology Group will work on Blue Gene and the protein folding grand challenge. IBM also plans to involve leading genetic scientists from academia and industry, Horn said.

IBM is in talks with drug makers Aventis <HOEG.F> <RHON.PA> <RP.N>, Bristol-Myers Squibb Co. <BMY.N> and Merck and Co. Inc. <MRK.N> and medical researchers at the Massachusetts Institute of Technology, the Toronto Hospital for Sick Children and Columbia-Presbyterian in New York, he said.

((-- Eric Auchard, New York newsdesk, 212-859-1840))