Linux plays role in smallpox investigation

The Center for Disease Control in Atlanta is using distributed Linux clusters to help break down the genetics of the smallpox virus, with the goal of creating a better vaccine for the pathogen.

The need for a new smallpox vaccine arose when it was discovered recently that the vaccine used today to inoculate military and healthcare workers can be harmful, or deadly, to a small percentage of those who receive it. (A government campaign to vaccinate nurses and soldiers began this year as a precaution against potential bioterrorism attacks).

The CDC’s Biotechnology Core Facility Branch is using the Evolocity supercomputing cluster of Linux nodes from LinuxNetworx. The cluster of machines is used to run simulation programs to study how smallpox attacks the human body, alongside other applications used to simulate and predict how the virus might react to different types of vaccines.

Some operations – simulations and genetic decoding applications – that once took two weeks to run on nonclustered processors at the CDC can now be completed in a single day on the clustered Linux system, the agency says.

Clusters of Linux machines running commodity Intel hardware are being deployed more as a cost-effective alternative to proprietary supercomputing or Unix clustering systems, used traditionally in areas such as scientific research. Such organizations as Lawrence Livermore National Labs, Sandia National Labs and NASA have used Linux clusters for supercomputing operations for several years.