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Feature - Asian computers join forces against avian flu

Feature - Asian computers join forces against avian flu


Computer simulation of potential drug candidate attacking avian flu virus. Image courtesy Dr. Ying-Ta Wu, Academia Sinica, Taiwan

Dealing with deadly diseases is not just a matter of test-tubes and petri dishes. Increasingly, grid computing is being used to simulate the ways that new drugs could attack viruses, looking for a magic bullet that could cure diseases or even prevent epidemics.

Computers can simulate a large number of chemical compounds and measure their ability to fit snugly into the chemical coating of a virus, thereby blocking its ability to function properly. Launched in March 2009, this so-called "Avian Flu DC2 Refinement" is the latest attack on avian flu using grid computing power. This initiative is supported by the EUAsiaGrid community, a partnership of Asian and European research institutions co-funded by the European commission to foster new uses of grid computing for science and society, and coordinated by the Italian Institute of Nuclear Physics (INFN).

The drug compounds being tested in Avian Flu DC2 Refinement are the results from a previous run of computer-aided chemical analysis, called EGEE DC2. In 2008, EGEE DC2 finished processing 300,000 molecules for eight new avian flu mutation targets. Academia Sinica Grid Computing (ASGC), a key actor in the EUAsiaGrid partnership, extracted from these results 20,000 high-scoring compounds (drug molecules that looked likely to have an effect) for the DC2 Refinement.

In addition, ASGC also assisted all Asian partners in setting up the necessary IT infrastructure service to share their computing resources in a secure and efficient way. This involved setting up a Certification Authority together with Registration Authorities in the participating Asian countries, as well as establishing an EUAsia Virtual Organization (VO) and deploying the Grid Application Platform (GAP) Virtual Screening Service (GVSS) over the EUAsiaGrid infrastructure. GVSS is an application package that integrates the EGEE gLite software DIANE2 and AMGA and employs Autodock as the simulation docking engine. Within the GVSS, the EUAsiaGrid users could upload their compounds and targets, submit massive grid jobs and run docking processes over EUAsia VO computing resources. Furthermore, the progress of job execution can be remotely monitored and the results directly displayed in GVSS..

Grid computing works much faster than checking 300,000 petri dishes. Image courtesy Dustin Day, stock.xchng

Joining forces

The grid technology allowed 125 processor cores - the heart of every computer - to join forces even though they were thousands of miles apart, in computing centers in Taiwan, Thailand and Malaysia, to name a few. During three weeks, users from Taiwan, the Philippines, Thailand and Malaysia subscribed to the service and submitted computing jobs over GVSS to the EUAsia VO. All the computing jobs were completed within four weeks. A total of 1,111 CPU-days were used, which is equivalent to running a single computer for over three years. Over 160,000 files generated a large volume of data, about 12.8 gigabytes, which was collated in a database.

In the future, thanks to efforts such as those of the EUAsiaGrid community, biomedical experts will be able to use the newly gained information to guide their search for better drugs to combat avian flu, and save them many costly false starts. Already, the community is gearing up for the next big challenge, which focuses on finding drug candidates to combat the virus behind dengue fever, a disease which threatens billions around the world. Like bird flu, this is a disease of particular concern to Asia: around 95% of the 50 million cases diagnosed each year happen to children under 15 in South-Eastern Asia.

-Francois Grey reporting for EUAsiaGrid

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