Grid Computing Spreads to SARS

By Kristen Philipkoski

A distributed-computing project harnesses volunteer computers in a project much like Seti@home to test drugs that might help curb severe acute respiratory syndrome.

The project uses computers' idle time to create a supercomputer capable of using models to rapidly test the effectiveness of potential drugs to fight the SARS virus. Sans promotion, 15,000 computer users have already downloaded the D2OL software that allows them to donate their processing power to search for a cure for SARS.

SARS has infected 5,462 people worldwide and killed 353. While several countries such as Canada and Vietnam have got the virus under control, China and Hong Kong still struggle with its spread. Containing the disease may be impossible at this point, and a treatment is desperately needed.

"The site has been working very slowly because, much to our pleasant surprise, this thing has gone viral," said Bonnie Gould Rothberg, medical director of the Rothberg Institute for Childhood Diseases, which now runs the project. "We're upgrading as fast as we can."

Initially, the Rothberg Institute adopted the D2OL distributed computing platform to search for cures for rare childhood diseases. But when SARS reared its ugly head, it caught Gould Rothberg's attention. She is a native of Canada, where SARS has killed 20 people.

Sengent, a Boca Raton, Florida, company that writes distributed-computing software, launched the D2OL project to search for cures for smallpox, anthrax and Ebola after Sept. 11 when those pathogens were identified as prime suspects for bioterrorism.

Distributed computing, also called grid computing, can screen potential drugs much faster than researchers in a laboratory.

"They (researchers) can't in a short time screen millions of compounds, but on the computer you can," Gould Rothberg said.

The Rothberg Institute's involvement started with a coincidence: Dr. Jonathan Rothberg, chair of the Rothberg Institute and CEO of biotech company CuraGen, happens to have a nephew who is also the chief technical officer at Sengent. Rothberg asked his nephew, Gioel Molinari, if distributed computing might help find treatments for rare childhood diseases like tuberous sclerosis. Within 48 hours, Molinari had a platform up and running for the institute. The program has led to at least one clinical trial.

The Rothberg Institute took over management of all of the D2OL projects, including the bioterror searches, about six months ago, and began the SARS effort just a few weeks ago.

Many people who had volunteered their computers to find a treatment for tubular sclerosis have temporarily switched to supporting the SARS effort, said Tian Xu, a professor of genetics at Yale University as well as a scientific adviser at the Rothberg Institute. Since the impact of SARS has been so devastating, it makes sense for other searches to be put on hold, he said.

When the project comes up with a promising lead, collaborating scientists in Shanghai take the molecules into the lab for testing.

Researchers there use petri dishes to grow samples of the SARS virus that were taken from patients. Xu is also a visiting professor at the Fudan University in Shanghai, where the research is going on.

"It is absolutely essential that we test our compounds against varieties of SARS that can cause disease in patients," Gould Rothberg said. "Our collaboration with the Fudan University will allow us to accomplish this goal."

Xu is working with the Fudan researchers to test potential SARS treatments, including drugs that are already approved for other diseases as well as Chinese herbs. The D2OL project hasn't come up with any leads yet, but Xu said many molecules remain to be tested.

"We need to screen many more compounds in order to find an effective one," said Xu. "We would like to screen 1 million compounds."

After promising compounds are pinpointed, they'll be ranked in order of how likely they are to work, and the Shanghai researchers will test them in that order.

"We don't know where this thing will go," Xu said, "but since SARS is so bad, we have to put our effort into it."