Stanford Cluster to Bridge Sciences

By John Taschek  |  Posted 2003-06-09 Print this article Print

Stanford University is using supercomputer clusters as a way to bridge the once-isolated disciplines of physics, biology and engineering.

Stanford University is using supercomputer clusters as a way to bridge the once-isolated disciplines of physics, biology and engineering.

Vijay Pande, an assistant professor of chemistry at Stanford who spearheaded the project, said 20 to 40 research groups across several disciplines will be using the cluster. The groups will be housed in the new Bio-X lab scheduled for completion this summer.

Bioinformatics will be among the first applications to leverage the cluster, according to Pande, in Stanford, Calif. Specifically, researchers will use the cluster technology to study and model protein structures and dynamics (also known as "protein folding").

Protein folding—a fairly new science—models the process in which proteins assemble themselves from their initial, unfolded (or "random coil") state of amino acids. In the mid-1990s, scientists theorized that protein misfolding leads to several diseases, including muscle degeneration, Mad Cow disease, and Alzheimers and other age-related diseases.

The problem facing scientists is that proteins fold naturally in fractions of seconds. Modeling the data points, therefore, requires massive amounts of data, and thats where supercomputer clusters come in.

One user of the new cluster is Tanya Raschke, a postdoctoral fellow studying structural biology at Stanford. Raschke is studying the chemical interactions in proteins and small molecules, as well as the interactions between proteins and surrounding water molecules.

Raschke said simulations that took as long as three days to run on an older computing cluster made up of Advanced Micro Devices Inc. Athlon-based systems will take a half-day to run on the new cluster.

As the director of eWEEK Labs, John manages a staff that tests and analyzes a wide range of corporate technology products. He has been instrumental in expanding eWEEK Labs' analyses into actual user environments, and has continually engineered the Labs for accurate portrayal of true enterprise infrastructures. John also writes eWEEK's 'Wide Angle' column, which challenges readers interested in enterprise products and strategies to reconsider old assumptions and think about existing IT problems in new ways. Prior to his tenure at eWEEK, which started in 1994, Taschek headed up the performance testing lab at PC/Computing magazine (now called Smart Business). Taschek got his start in IT in Washington D.C., holding various technical positions at the National Alliance of Business and the Department of Housing and Urban Development. There, he and his colleagues assisted the government office with integrating the Windows desktop operating system with HUD's legacy mainframe and mid-range servers.

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