Grid (un)Lock: Using a Data Grid to Fight Avian Flu


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Article ImageA one-year global initiative may prove to be not only a vital step in developing a vaccine for avian flu and other viruses but also a revolutionary scientific method. A research team with members from the University of California, San Diego and the University of Hawaii, along with people in Japan, Korea, and China, will use bioinformatics, grid computing, and networking infrastructure to understand the molecular structure of the virus.

“What we want to do,” says Peter Arzberger, principal investigator, “is to try to quickly tease apart and understand what it is we’re dealing with at a molecular level and then be able to design inhibitor drugs.”

The research team plans to take advantage of a variety of software tools that have already been developed and put them together in a way that will provide new insights. While the initial research will focus on how the avian flu virus is arranged genetically, Arzberger says the ultimate goal is to be able to have the computer infrastructure in place that will be applicable to a broader range of scientific inquiry.

Another goal of this project is to take advantage of a set of collaborations established through an earlier project called PRAGMA, which involved thirty institutions. “We want to link and integrate the set of tools developed in PRAGMA into this infrastructure, which will allow us to gain better insights more quickly,” says Arzberger.

For example, he says, in order to share data across the collaborating sites, the group is using a tool developed in Japan. To schedule resources to compare the structure analysis, a program is being developed in China. Korea is providing the knowledge for a secure web interface.

“It’s an opportunity to integrate or harvest the various tools that have been developed separately into an environment where we can really analyze avian flu or the next influenza,” says Arzberger. “If there’s a good tool out there, we should take advantage of it. We don’t want to have to reinvent things that work well.”

The collaboration shows the growing importance of global cooperation. A pandemic is not isolated to one country or one section of the world. The research is funded through an arm of the Department of Defense—the Telemedicine and Advanced Technology Research Center (TATRC)—because, according to Arzberger, as the military is sent to various areas of the world, soldiers are more susceptible to being exposed to viruses.

The scientists will use a suite of bioinformatic software called integrated Genome Analysis Pipeline (iGAP) to analyze the avian flu genomes. The researchers will run computer simulations to identify the active sites where molecules will dock. “We’re looking for the places where the molecules are turned off,” Arzberger explains. They will then look for the molecules that are the best candidates to be inhibitors.

Arzberger adds that it is important to look at the project as the future of “doing science.” The IT infrastructure allows for a new type of collaborative team science. “You have to do this type of science because of the types of problems we’re going to be dealing with. No one country has all the resources necessary. This project is an example of how we’re able to interact.”

By the end of the year-long project, Arzberger hopes his research team will be able to provide the answer to the question, “Can we, through this better set of tools, come up with a better understanding of what could inhibit the spread of this disease that will ultimately lead to drug design?”

(www.pragma-grid.net; www.tatrc.org)