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Stanford partner in new effort to revolutionize high-performance computing

Two Stanford projects have been chosen to participate in a new effort to upgrade the nation's high-performance computing environment. On March 28, the National Science Foundation selected a consortium headed by the University of California-San Diego (UCSD) to implement the five-year effort, valued at up to $170 million.

Russ B. Altman, an assistant professor of general internal medicine, and computer scientist Hector Garcia-Molina, the Leonard Bosack and Sandra K. Lerner Professor in the School of Engineering, head the two Stanford projects represented in the consortium, called National Partnership for Advanced Computational Infrastructure (NPACI). Altman's project centers on analyzing the architecture of large biological molecules. Garcia-Molina heads the Stanford Digital Library project, which has the goal of uniting the varied information sources available on the Internet into a single virtual library system.

The purpose of the project is to develop the infrastructure that the nation's scientists need to tackle currently intractable scientific and engineering problems, such as climate and weather prediction, complex drug design and the creation of new materials with desired characteristics.

"Over the next several years, the partnership intends to create a national metacomputing environment, which will consist of geographically separated high-performance computers, data servers, and archival storage and visualization systems linked by high-speed networks so that their aggregate power may be applied to the most complex research problems that cannot be studied any other way," according to the news release issued by the University of California-San Diego.

NPACI includes 37 research institutions and builds on the San Diego Supercomputer Center established at UCSD in 1985. The other California participants include California Institute of Technology; Lawrence Berkeley and Lawrence Livermore National Laboratories; and the University of California's Berkeley, San Francisco, Davis and Santa Barbara campuses.

Altman is a member of the steering committee at the San Diego Supercomputer Center, where he has been a user for the last 10 years. "The focus of the NPACI grant on molecular science and digital libraries fits perfectly with parts of my research in the analysis of protein structure and function, as well as with my interests in new ways of representing the published biomedical literature," Altman said.

With the new support, Altman will adapt algorithms for analyzing molecular structure so that they will work with massively parallel computers. This will make these tools available to biologists around the world. In addition, he and his long-time collaborator at the supercomputer center, Phil Bourne, will combine some of the tools that they have been working on in order to achieve better performance and a wider range of functionality.

The Stanford Digital Library project was started in 1994 with funding from the National Science Foundation, the Defense Advanced Research Projects Agency and the National Aeronautics and Space Administration. Its goal is to develop the technology required to integrate the broad range of information repositories available over the Internet into a universal, virtual library system.

"We will work with other NPACI partners to apply the technologies developed under the original Stanford Digital Library project to support interoperation of the various digital libraries developed for NPACI," Garcia-Molina said. A large number of information resources, services and libraries will be developed as part of the new effort. So it is particularly important that they be accessible in a consistent way.

For more information, on the World Wide Web:
Executive summary of the NPACI;
Scientific American article on Altman's research on medical information
Russ B. Altman's home page
Stanford University Digital Libraries Project
Hector Garcia-Molina's home page


By David F. Salisbury