Understanding the nuances of infectious diseases—in particular malaria, which killed about one million people worldwide in 2008—is a crucial step toward wiping them out. However, getting a clear picture of how malaria spreads and how it responds to eradication efforts means accessing a daunting amount of data from a variety of sources, the type of job best suited to a number-crunching supercomputer.

Supercomputers, once the privilege of a select few universities and government laboratories, have become redefined in recent years so as to make them more accessible to smaller research labs as well. This includes a team from Intellectual Ventures in Bellevue, Wash., that is taking advantage of the speed and power of a supercomputer brought online over the past year to create complex simulations they hope will reveal solutions to complex problems, including the spread of malaria.

Intellectual Ventures' supercomputer is a work in progress that is shared by two different teams of researchers within the organization—one studying malaria (pdf) and the other, called TerraPower, studying nuclear reactor technology. The malaria project got off the ground in 2007, after the Bill and Melinda Gates Foundation called upon Intellectual Ventures to develop new technologies to fight malaria. This spawned the idea of using computer models to simulate the spread of the disease worldwide.

The supercomputer consists of 138 Dell blade servers running multiple processing units (or cores) on each server, for a total of 1,104 cores. Intellectual Ventures generally devotes 1,024 of those cores to TerraPower and the rest to its malaria research. The researchers chose Microsoft Windows as its operating system (Linux is also commonly used in supercomputing clusters) because the system administrators at their facility are familiar with Microsoft software. It did not hurt that Microsoft co-founder Bill Gates is investing in both the TerraPower and malaria projects, and that Intellectual Ventures itself was formed by former Microsoft executives Nathan Myhrvold and Edward Jung.

The supercomputer, which has five terabytes of memory and 30 terabytes of storage, supplies the brute power to crunch numbers, but this would mean little without the software to instruct the computer. The software pulls biological data on the behavior and reproductive rates of the Plasmodium parasites and the mosquitoes that carry them, as well as information on infection patterns and immune responses among humans. Other data include where people live and how they travel, environmental factors (temperature, rainfall and elevation) that are important to malaria transmission, and the locations of different species of mosquitoes. The software uses this data from a variety of sources—including the World Health Organization, Malaria Atlas Project, universities and NASA—to create models of how malaria outbreaks play out.

Before the supercomputer became available last year, the malaria project researchers used an eight-core computer to establish the basics of their research. They needed to expand their computing power, however, to more accurately model the disease over larger geographic areas. "A larger cluster means you can simulate larger areas in the same amount of time," says Philip Eckhoff, a research scientist at Intellectual Ventures. The team uses the Monte Carlo approach to create its malaria simulations, relying on information from repeated trials to build results. As such, access to more cores allows the researchers to run more trials faster and reach their target number of trials sooner.

1 Comments

1. 1. Bob_541 02:35 PM 5/21/10

   Yesterday GlaxoSmithKline made available, in the cloud, and for free to all, the Tres Cantos Antimalarial Set (TCAMS) of more than 13,500 screened compounds with activity inhibiting the Malaria parasite. It can be accessed through the cloud based chem. Informatics database of
   Collaborative Drug Discovery http://www.collaborativedrug.com/

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