Feature - Dealing with dengue
First, you get a bad headache. Then your joints feel like they are being crushed. This is followed by fever and a bright red rash on your legs and chest. You may also start vomiting or have diarrhea. This is dengue fever, and it affects two-fifths of the planet’s population. Thanks to the EUAsiaGrid project, grid technology is doing its part to help reduce the burden of this devastating disease.
For most, dengue fever passes after a very unpleasant week, but for some it leads to dengue haemorrhagic fever, which is often fatal. Like malaria, dengue is borne by mosquitoes. Unlike malaria, though, it affects people in cities as much as in the countryside. As a result, it has a particularly high incidence in heavily populated parts of South–East Asia, where it is a significant source of infant mortality in several countries.
As yet, there are no drugs that specifically tackle the dengue virus. So the goal of an initiative called Dengue Fever Drug Discovery, launched last July, was to start a systematic search for such drugs, by harnessing grid computing to model how huge databases of chemical compounds would interact with a key replication factor of the dengue virus, potentially knocking it out of action.
This is not the first time that grid technology has been used to amplify the computing power that can be harnessed for such ambitious challenges: malaria and avian flu have been targets of previous massive search efforts, dubbed by experts “in-silico high-throughput screening.”
Leading the effort for dengue at Academia Sinica in Taipei is researcher Ying-Ta Wu, of the Genomics Research Center. He and his colleagues prepared some 300,000 virtual compounds to be tested in a couple of months, using the equivalent of over 12 years of the processing power of a single PC.
Benefits of research
The goal of this exercise, though, was not just to get the processing done quickly. It was also about encouraging partners in Asia to collaborate on sharing the necessary hardware.
These included Universiti Putra Malaysia and the MIMOS Berhad Institute in Malaysia, the Institute of Applied Mathematics and Informatics in Vietnam and the Hydro and Agro Informatics Institute of Thailand, as well as CESNET, an academic network operator in the Czech Republic.
The successful collaboration is a testament to efforts by the EUAsiaGrid project, led by the Academia Sinica Grid Computing Center in Asia and INFN in Italy, to attract new partners in South-East Asia to grid computing, and to train them in how to deploy and run the necessary middleware in their own institutes. In this case, the GAP-based Virtual Screen Service (GVSS) was used — an application package that combines the EGEE gLite middleware with a drug docking simulation package called Autodock.
“We will have to wait a while to judge the final result of this effort,” says Ying-Ta Wu. Indeed, after sorting out the most promising drug candidates, researchers must now begin the arduous task of testing these drugs on real viruses. And even if successful candidates are found, there is still a long way to a product that can be safely administered to people suffering from dengue.
But at least, thanks to grid computing, an important first step has been taken down that road.
—François Grey, for EUAsia Grid