An IBM supercomputer directly related to the famous Deep Blue
that battled chess grand master Gary Kasparov in 1997 has recently
been recruited to aid Canadian researchers in the fight against
cancer.
One of the biggest challenges in our research is being able to
sort through a large volume of data.Igor Jurisicaprofessor of
computer science and biophysics at the University of
TorontoText
The Life Sciences Discovery Centre of the University Health
Network (UHN) in Toronto is using an IBM eServer p595 supercomputer
to analyze protein interactions.
These interactions are vital to the understanding of cancer
biology at the molecular level. The process is crucial to charting
a tumour's progression and ultimately developing treatment.
The UHN centre received the supercomputer along with IBM's
WebSphere Information Integrator server application and DB2
database software under Big Blue's Shared University Grant program.
The package is worth more than US$2.5 million.
"One of the biggest challenges in our research is being able to
sort through a large volume of data," said Igor Jurisica, a
scientist with the Ontario Cancer Institute of the UHN. Jurisica is
also a professor of computer science and biophysics at the
University of Toronto.
With a lesser computer, Jurisica estimates his calculations
would take months but with the p595, they can be accomplished in
weeks or days, shaving wait times by 50 per cent. "With 120,000
known proteins and 25,000 to 30,000 we're looking at millions of
possible interactions. You can see we have quite a real big hair
ball."
The p595 supercomputer used by the UHN "is a descendant of Deep
Blue" that famously trounced Kasparov in a series of man versus
machine chess matches in 1997, according to Don Aldridge, IBM
Canadab s general manager for higher education, research and life
sciences.
Deep Blue was a 1.4-ton IBM RS/6000 SP high performance computer
that had 256 Power2 processors. It was specifically created to play
chess and could explore 200,000,000 positions per second. At the
time of the match Kasparov could explore approximately three
positions per second.
Deep Blue technology was eventually used to tackle other real
world problems such as forecasting weather patterns.
"In the case of Deep Blue it was a natural progression to evolve
from predicting chess moves to predicting hurricanes because in
both cases you are dealing with multiple variables," said Dave
Marks, consulting director for the research and consulting firm IDC
Canada Ltd.
According to Marks, the desktop-sized p595 supercomputer
inherited a lot of properties from Deep Blue "but is much faster in
terms of computing capacity and consumes less power."
Aldridge said p595 can be configured in different ways to deal
with specific situations, but that the UHN is "stretching it in
ways we would not have thought possible."
Learning is a two way street, said Aldridge. "When scientists
like Igor [Jurisica] come to the IBM Lab it gives our researchers a
chance to work with our equipment in real world situations."
Marks said IBM is working on another supercomputer project
dubbed Blue Gene with the mission of studying molecular functions
and protein folding.
Proteins react with each other in varied ways. Jurisicab s team
is trying to determine which patterns are disruptive or prone to
cause tumours.
Molecular profiles of cancers help detect signs that
pathological tests might have missed at the tissue level, Jurisica
said. "For instance, it is known that women with mutations in their
BRCA1 and BRCA2 genes are predisposed to breast and ovarian
cancer."
However, he cautioned that it is not a black and white
situation. "By tracing protein patterns and factoring in variables
such as medical history, habits and environment, we could determine
whether the person is simply predisposed or if cancer is already
present."
This determination, Jurisica said, could spell the difference
between providing early aggressive treatment and needlessly
lowering the standard of life exposing the person to unneeded
medication.
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