PC grids to power hunt for new drugs

The humble personal computer used to send email or surf the internet could quietly be finding a way to stop cancer, treat smallpox or counter a bio terror attack with anthrax spores.

    PC grids can match powerful supercomputers

    Of limited power on their own, PCs 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

    centre 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.

    "Frankly at the moment I think we are limited more by our

    imaginations that we are by the technology"


    Mike Brady,
    information engineering professor at Oxford University

    "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.

    Supercomputers

    United Devices (UD) rents out time on a commercial grid

    which it assembled from 7000 personal computers, a network that

    Kirchoff said ranked among the world's top eight supercomputers.

    That is dwarfed by the 2.5mn computers hooked up to a

    global grid (www.grid.org) 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 $75mn

    on the cheapest conventional hardware, Kirchoff said.

    Research

    Novartis is among the growing number of drug makers using

    in-house grids to search for new drugs.

    It has 2700 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.

    Experts say powerful computers
    will never replace human genius

    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.

    Treating diseases

    "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 centres, 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.

    SOURCE: Reuters


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