Networking Computers to Help Combat Disease

According to this article, in 2005 there were about 350-500 million infections and approximately 1.3 million deaths due to malaria. In addition, Dengue struck approximately 200,000 people, almost 1,200 of whom died from the disease. Despite this evidence, "these diseases are comparatively neglected by large pharmaceutical companies", and high-technology solutions are often only available to developed nations, the author argues.

As detailed here, Grid computing (see Wikipedia for one definition) is being used as a tool in developing countries worldwide to find a cure for subtropical diseases. The strategy involves using information and communication technology (ICT) to stimulate new approaches to collaborative large-scale science, to discover new drugs, and to better understand the nature of diseases such as malaria and Dengue.

Centrally, Grid technology is meant to be a means for speeding drug discovery by increasing access to information. The author explains that the current research process involves seeking compounds that can inhibit or kill invading parasites and infections, but there are potentially millions of such candidate compounds; thus, it can take 10 years to discover a drug and another 10 to get it approved. In contrast to these in vitro and in vivo approaches, with this new type of Grid-based research, it takes between a few seconds and a few minutes to model a possible match between a protein from the malarial parasite to a ligand (chemical compound that binds to protein receptors).

For example, using the FlexX software developed at the Fraunhofer Institute and donated by the BioSolveIT company, Wide In Silico Docking on Malaria (WISDOM) used its own Enabling Grids for E-sciencE (EGEE) Grid to match 3-dimensional structures of proteins to ligands, performing the equivalent of 80 central processing unit (CPU)-years of calculations in just 6 weeks. Analysis of WISDOM results found that the 1,000 most promising compounds out of 1 million candidates could be selected using a relative ranking scale between different ligands, "which demonstrated the validity of the approach."

To cite an example of the use of Grid beyond drug discovery, the Africa@home project (click here for details) allows people to donate idle CPU cycles in a distributed infrastructure to perform epidemiological modelling. The author claims that this approach enables researchers to calculate the impact of vaccines, for example, or the spread of a disease. One scientist quoted in the article explains that Grids "could also be used to federate databases collecting data on infection and treatment in malaria and Dengue, but also in HIV. This is vitally important information that is currently very difficult to collect in Africa."