CDC Uses Linux Cluster To Study Smallpox

Although much of the world's attention has been focused on treating and containing the outbreak of severe acute respiratory syndrome, or SARS, the Centers for Disease Control and Prevention is still devoting IT resources to protect the country from the threat of a smallpox outbreak.

Since the beginning of the year, the CDC's National Center for Infectious Diseases has been using a Linux cluster to run bioinformatics programs that will help scientists better understand smallpox, a contagious, infectious disease for which there is no specific treatment. The cluster consists of 40 Athlon MP processors from Advanced Micro Devices, Evolocity rack-mounted servers from Linux Networx, and several Ice Box appliances, also from Linux Networx. The Ice appliances combine a serial terminal server and a remote-controlled power switch to simplify cluster management.

The Linux cluster is the first of its kind within the CDC, which is still officially a Windows shop. But Linux is the cheapest and most-effective way to cluster servers, says one of the center's bioinformaticians. A bioinformatician is an IT professional whose work includes developing mathematical codes for analyzing, managing, and processing biological data. The ability to use AMD Athlon MP processors within the cluster helped keep the cost at about $60,000.

"There's a lot of bioinformatics software that runs on Linux and a lot of development and management tools that, likewise, were written for Unix," the bioinformatician says. For example, the cluster is running programs that study the phylogeny, or evolution, of the smallpox virus. These programs compare different variations within the smallpox virus with the hope that vaccination and treatment for smallpox will evolve as the virus itself evolves.

"Our goal is to understand as much as we can about smallpox," the bioinformatician says. As such, the center is devoting a portion of its IT resources toward accumulating knowledge that it hopes it will never have to use.