CDC using cluster to study smallpox

Centers for Disease Control and Prevention smallpox Web page

The Centers for Disease Control and Prevention are using a cluster supercomputer to study smallpox genomics and vaccine interactions.

The Linux Networx Inc. Evolocity cluster links 40 computer processors, allowing scientists to whip through bioinformatics problems such as smallpox genomic functions, which aid in new vaccine development, company spokeswoman Andrea Bingham said.

"It's imperative to get information crunched faster so they can get on with creating cures," she said.

CDC's Biotechnology Core Facility Branch has been using the cluster since September, and genomic functions that may have taken one computer two weeks to complete are finished in a day, Bingham said. The cluster is running programs such as BLAST, or Basic Local Alignment Search Tool, which determines the functions of newly discovered genes.

Using a cluster is more cost-effective than building a new supercomputer and much faster than running complex programs on one computer, Bingham said. The cluster also costs about one-tenth less than a traditional supercomputer.

The Linux cluster includes management tools that enable administrators to keep a close watch on each node in the cluster. For example, the tool can monitor the temperature of the computer and the available memory, alerting administrators of any hazards and turning off the affected node, Bingham said.

"They can just let the tools run, and they can concentrate on the genome sequencing and the study and not what's happening on Node 12," she said.

The cluster can be used for other research areas, said Eric Pitcher, vice president of product marketing, government, industrial and life sciences.

Bioterrorism threats have caused officials to re-examine giving the smallpox vaccine, which hadn't been administered since the 1970s. Certain military officials and first responders have been ordered to receive the vaccine, which can have deadly side effects. Such concerns have led CDC officials to study new vaccines.

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