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Supercomputing and the fight against H1N1

OSC sent us news this week about a researcher at The Ohio State University who has been using OSC’s supers to develop a new application to track and analyze the genetic codes of swine flu virus as it travels the world, moving from host to host and mutating to resist antiviral drugs.

Supramap application imageIn a journal article published in the April 2010 online issue of Cladistics, Daniel Janies, Ph.D., explains how Supramap (http://supramap.osu.edu) was created to track the avian influenza virus (H5N1) and, more recently, to monitor the H1N1 virus. Cladistics refers to the scientific classification of living organisms, based on common ancestry, into evolutionary trees. Evolutionary trees are used by many researchers studying infectious diseases to understand the geographic and host origins of pathogens and how the pathogens change over time. Supramap puts phylogenies in a geographic context as well.

“The integration of our core phylogenetic reconstruction codes with Supramap has allowed an entirely new way to view linked evolutionary and geographic information,” said Ward Wheeler, a coauthor of the article and curator-in-charge of scientific computing at the American Museum of Natural History (AMNH). “The Supramap tool set has broad utility not only in tracking human disease in time and space, but historical patters of biodiversity and global biotic changes.”

This is one of those applications that just screams for someone to think hard about how to make it available to non-HPC specialists.

Janies and his colleagues used a small cluster computer at OSU to beta-test the Supramap application, which has been developed through a grant from the Defense Advanced Research Projects Agency (DARPA).

The research team also adapted the Supramap code to function smoothly on the OSC’s flagship IBM Cluster 1350 “Glenn” system, which features 9,500 cores and 24 terabytes of memory. They now are working with the Center’s staff to finish development of a Web interface to provide easy Internet access to the application by scientists and public health officials.

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