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The humble PC joins search for smallpox cure

The power of home PCs is being combined to help laboratory researchers fight disease

Mark Samuels, Computing 15 Oct 2003
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The PC is now so ubiquitous that it is easy to forget that Computing was already a strapping eight-year-old before it made its debut.

What is even easier to overlook is the continuing advance of applications and technology. For example, PC power has been harnessed through powerful networks, to create the basis of a global supercomputer that is being used to help find a cure for some of the world's most deadly diseases.

These advanced research networks are a long way from the humble beginnings of the PC, which began on 12 August 1981, when IBM first introduced the Personal Computer.

Continued growth over the next 20 years has seen the PC adapted by hardware providers and adopted by companies throughout the world.

Analyst Gartner estimates there will be 161 million PCs shipped worldwide during 2003.

The vast number of users means the PC remains at the heart of most business and home networks, despite the increased importance of PDAs and tablet computers.

And because of the prevalence of desktop computing and the growth in processor speed, memory and storage, new strategies are still being developed to make the most of the PC's power. One example is grid, or distributed, computing, where many PCs are applied in a network to solve a single problem at the same time.

One of the highest-profile examples of the technology in action is the Smallpox Research Grid Project, which draws on the resources of home PC users to try to find a cure for the disease.

'The desktop computer is a massive computational resource and the gains in PC performance have been revolutionary,' says Guy Grant, of the department of physical and theoretical chemistry at Oxford University.

The smallpox project follows a similar principle to SETI, the Search for Extra-Terrestrial Intelligence research project.

Users download a screensaver that activates when the computer is idle. Smallpox data is sent via the internet and processed using the PC's spare power. All data is sent back to Oxford University for further analysis.

The university has already developed two similar grid-based initiatives. Its project to discover anti-cancer drugs and its attempt, from spring 2002, to find drugs to block anthrax, demonstrated how grid computing could unite a community of up to two million users in a very short time.

Oxford's latest grid uses the spare capacity of desktop PCs to find a drug-based cure for smallpox. Although there is a vaccination to prevent smallpox, there is no known cure for the disease post-infection.

What's more, a vaccination is dangerous for certain at-risk groups, including pregnant women, young children and HIV patients. A smallpox drug would carry less risk. It could also be administered as a localised cure in the event of a terrorist attack.

Oxford's virtual screening project is looking for a drug from about 35 million possible chemicals. Molecules are screened and an attempt is made to fit them to a potential target.

'The target is a bit like a glove,' says Grant. 'The disease we're trying to block fits totally into this glove - and it's a pretty tight fit.'

Two-and-a-half million PC users have registered so far. 'We depend on goodwill - and people enjoy the idea of helping the rest of the world,' says Grant.

Progress has been swift and the smallpox grid screening is due to be completed this month. As many as four or five per cent of the screened molecules could be potential smallpox drugs.

Further analysis of these molecules will reduce the dataset further - but it's too early to say if Grant and his Oxford colleagues will find a cure.

'We haven't looked at the data in detail yet because the analysis tools we're planning to use need to look at the dataset as a whole,' he says.

A separate spin-off company has been developed to deal with the intellectual property created through Oxford's earlier cancer project, but the results of the smallpox scheme will be delivered to the US Department of Defense.

Results will soon be appearing and Grant says grid computing has been invaluable.

'Having access to this resource gives access to a much wider range of molecules,' he says. 'It speeds up the screening process and we might be able to speed up the drug discovery rate by two or three years.'

Grid computing allows Oxford to send out small batches of data to millions of individuals to process information on home PCs. IBM provides Unix servers and DB2 database software for the central infrastructure, which is linked to the PCs using specialist software from supplier United Devices.

Grant offers just one concern about the growth of grids. 'Definitely get involved if you can think of a suitable project,' he says. 'But please don't take our user base.'

See also:

Distributed computing boosts efficiency by putting spare PC or server capacity to good use.  26 Nov 2003
30 years of digital Britain  16 Oct 2003

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