Stanford Report, February 16, 2001
BY MARK SHWARTZ
This month's landmark publication of the human genome -- the so-called "genetic book of life" -- is expected to revolutionize biomedical research in the 21st century.
But the genome map is only the beginning. The next challenge will be determining the function of each of the 30,000 to 40,000 genes that make up human DNA -- as well as the hundreds of thousands of proteins those genes produce.
Unraveling the secrets of the genetic code will require massive computing power beyond the capacity of ordinary PCs.
The Origin 3800 - which
marks the beginning of a new Stanford-SGI partnership in
biomedical supercomputing - will be dedicated exclusively
to solving complex problems in biomechanics, genetics and
other biosciences.
Photo: Courtesy of SGI
Enter biocomputation -- an emerging field that uses powerful computers to solve complex problems in genetics, protein analysis, biomechanics, surgical planning and other biosciences.
Stanford--SGI partnership
Biocomputation at Stanford took a giant leap forward on Feb. 16 with the unveiling of an SGI Origin 3800 supercomputer -- the latest high-speed processor manufactured and designed by SGI (Silicon Graphics).
"The Origin 3800 marks the beginning of a new Stanford--SGI partnership in biomedical supercomputing," said Charles Taylor, assistant professor of surgery and, by courtesy, of mechanical engineering, during Friday's press conference in the Gates Building.
"It's now the biggest computer at Stanford and one of the largest at any university dedicated exclusively to biocomputation," he added.
Taylor was joined at the press conference by Charles H. Kruger, vice provost and dean of research and graduate policy; Russ B. Altman, associate professor of medicine and, by courtesy, of computer science; and Bob Bishop, chairman and chief executive officer of SGI.
"We are in a golden period of biomedical research," said Altman, director of the university's new Center for Biomedical Computation.
Altman noted that the Origin 3800 already has allowed one of his graduate students to reduce his average computation time from three months to just two days.
Taylor and Clay Anderson, a research associate in mechanical engineering, explained how the Origin 3800 can be used to create 3-D images to predict the rate of blood flow and muscular-skeletal movement in people.
Bishop pointed out that SGI's medical applications and core engineering groups have enjoyed a close collaboration with Stanford for many years.
"We believe that Stanford University is uniquely capable of making important discoveries in biocomputation because of its history, its vision and its comprehensive understanding of how to exploit visualization technology to enhance data interpretation," he said.
The press conference was followed by a media tour of the supercomputer, which is located in the bottom floor of the Gates Building.
Bio-X
The idea of having a supercomputer dedicated to biocomputation became a reality last spring when Taylor and other faculty members received a large grant from the Stanford Bio-X program -- a pioneering, campus-wide effort to encourage interdisciplinary research in biomedicine and biotechnology.
Bio-X was launched in 1999 with a $150 million donation from Jim Clark, founder of SGI, cofounder of Netscape and a former professor of electrical engineering at Stanford. The Bio-X program brings together researchers working in such diverse fields as biophysics, biochemistry, microbiology, chemical and mechanical engineering, computer science and surgery.
The $5 million Origin 3800 was purchased with a combination of funds from Bio-X, the School of Engineering, the School of Medicine and the Office of the Dean of Research along with an equipment donation from SGI.
The Origin
3800 is now fully operational and available to all
Stanford researchers involved in biocomputational
projects. For information, see www.stanford.edu/group/supercomputer/
