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DAILY NEWS AND INFORMATION
FOR THE GLOBAL GRID COMMUNITY /
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Applications:
VIRTUAL SUPERCOMPUTERS JOIN HUNT
FOR NEW DRUGS
The humble personal computer used to send e-mail or surf the Internet could
quietly be finding a way to stop cancer, treat smallpox or counter a
bio-terror attack with anthrax spores.
Of limited power on their own, PC's, when wired into so-called "Grids,"
mimic
the world's most powerful supercomputers, but at a fraction of the cost.
Networks of Internet-linked computers -- many in people's homes -- are
breaking the constraints that tight budgets and a lack of number-crunching
power once imposed on researchers' quests for important new medicines.
Computer mice have not replaced laboratory mice as the proving ground for
drugs, but the Grids are helping scientists in their hunt for them.
In essence, Grid computing parcels out tiny parts of a complex equation to
lots of remote computers that seek digital needles in haystacks and then send
the results back to the data center to be re-assembled in a useful form.
Grids can tackle in days complex problems that would take months or years
to
crack on costly conventional hardware.
The technique is perhaps best known from the SETI@home project that uses
millions of networked computers -- each examining just small samples of data
-- to search for extraterrestrial intelligence by poring over signals from
space.
"When you turn on so much power, science guys who have limited their
science
based on real budgets and departmental boundaries and everything else really
have to rethink what is truly possible," said Paul Kirchoff, vice president of
marketing at United Devices, a Texas firm whose software makes Grids run.
United Devices (UD) rents out time on a commercial Grid which it assembled
from 7,000 personal computers, a network that Kirchoff said ranked among the
world's top eight supercomputers.
That is dwarfed by the 2.5 million computers hooked up to a global Grid run
by
UD that crunches numbers for purely humanitarian causes, including the search
for drugs to treat cancer, smallpox and anthrax.
A lot of the Grid's machines -- half at big companies, half in individual
homes or offices -- get turned off at night or are portables that go on or off
the network, Kirchoff said, but the Grid in theory has peak power of just over
three petaFLOPS.
"To put that into perspective, it would be about 23 times the top 10
supercomputers in the world combined in terms of power. It is truly
phenomenal," he said.
UD accepts only non-commercial projects for that giant Grid, which depends
on
corporate sponsors to help defray costs.
The Grid approach works especially well for screening tens of millions of
known chemicals compounds to see if their shape lets them attach themselves to
-- and thus effectively switch off -- proteins that are known to cause
disease.
This whittles down huge chemical libraries to a few dozen promising
compounds
to be tested in animals and humans.
The Grid.org search for smallpox drugs, for example, reduced Oxford
University's library of 35 million compounds to 45 likely molecules in five
months, a task that would have cost up to $75 million on the cheapest
conventional hardware, Kirchoff said.
Enter The Virtual Chemist
Novartis is among the growing number of drug makers using in-house Grids to
search for new drugs. It has 2,700 PCs linked up now and aims to boost that to
between 20,000 and 25,000 within two years, said Manuel Peitsch, the head of
informatics and knowledge management at its drug research labs.
That would put the Swiss group's private Grid in the same ballpark as the
supercomputer that simulates earth's climate.
The first drug to be detected "in silico" is still years away from use in
humans, but promising compounds found by the Grid are now moving into the lab.
Peitsch said that is just the start.
In two years Novartis might be using the Grid as a virtual chemist to
design
targeted new drugs.
"You have fertile ground and once you have that fertile ground you can
start
thinking about processes you have never thought about before," Peitsch said,
such as simulating clinical trials or predicting how toxic new drugs might be
in humans.
Powerful computers will never replace a scientist's flash of brilliance
because you can't teach computers serendipity, he said, but the technology can
change the way researchers work.
"The big associations, the creative, crazy steps are taken by humans, not
by
machines," he said, but Grids let scientists focus on creative things while
machines do the drudgery.
Grid computing is also helping improve treatment of diseases such as breast
cancer by creating huge databases that specialists can comb efficiently for
useful information -- for instance guidance on whether a biopsy might be
warranted.
It was dream technology for Mike Brady, an Oxford professor of information
engineering who had wondered how to share batches of data on cancer patients
and still guard their privacy.
The e-Diamond Grid project set up by Oxford and IBM solved the problem.
Radiologists could compare mammograms from other cancer screening centers, not
just their own, creating a much more representative sample of cancer
cases.
"I didn't see any way in which we could overcome all of that but actually
the
Grid provides precisely the technology needed to do that," he said, adding
that the technology lends itself easily to studying other kinds of cancers or
brain disease.
"Frankly, at the moment, I think we are limited more by our imaginations
than
we are by the technology," Brady said.
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