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IBM’s Blue Gene Breaks New Research Ground

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With the interest in using supercomputing to advance medical science still
on the rise, IBM said a Japanese research laboratory will
use its Blue Gene/L machine to study proteins, hoping to create better drugs
to treat human diseases.

Big Blue Tuesday said the Tokyo-based Computational Biology Research Center
(CBRC) of The National Institute of Advanced Industrial Science and
Technology (AIST) will use Blue Gene/L to map out 3-D protein structures.

IBM declined to list financial terms of the contract. However, such
supercomputing pacts generally run in the millions of dollars.

William Pulleyblank, director of exploratory server systems at IBM Research,
said his group and AIST are also exploring possible areas for joint research
using software IBM has designed to tackle protein simulations on Blue

“We launched the Blue Gene project in 1999. At that time if we look at
the challenges of some of these things like protein folding in life
sciences, you’re going to have to do something different with a computer if
you want to attack these, Pulleyblank
told “We set out to build Blue Gene/L.”

Pulleyblank said when Blue Gene/L is installed in February 2005, the system
will consist of four rack machines, with 1,024 nodes per rack.

It will be based on IBM’s Power architecture and will
run at a peak processing speed of 22.8 teraflops, or trillions of
calculations per second. As of today, this would put it at No. 3 on the Top
500 supercomputing list.

Calling AIST’s choice of Blue Gene/L over other systems “validation that we
are getting this right,” Pulleyblank said the supercomputer will be 24 times
more powerful compared to the CBRC’s current computer systems.

Moreover, it uses about 1/10th the power per computation of and only
about 1/16th the floor space of most systems on the vaunted Top 500 list,
where IBM regularly butts heads with such rivals as SGI ,
Cray , HP , Sun Microsystems and Dell .

The AIST scientists are also creating high-performance computer applications for
molecular simulation, mass spectrometry analysis, and cell simulation.

Pulleyblank said that to make Blue Gene effective for disease research,
IBM’s researchers became well-versed in how genomes work, as well as the
complex topic of protein folding.

“What happens with proteins is you get things interacting in odd ways or not
behaving properly,” Pulleyblank said. “The first thing researchers try to figure out is why,
and the second thing they try to figure out is how to intervene to make it
stop misbehaving. With machines like Blue Gene we can do
that by studying the atoms that make up these molecules and do a custom
design of a drug that will respond to a specific mutation of a disease.”

IBM Research is getting a lot of mileage out of the Blue Gene project.
Pulleyblank said the Argonne National Laboratory in the United States and Dutch
astronomical group ASTRON will also be installing Blue Gene/L supercomputers
in 2005 to tackle scientific challenges.

Blue Gene/L is also part of the U.S. National Nuclear Security Administration
(NNSA)’s Advanced Simulation and Computing (ASC) Program, which IBM has been a partner of
since 2001. The NNSA will be installing a very large Blue
Gene/L system in 2005 at the Lawrence Livermore National Laboratory to advance understanding
of the behavior of materials.

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