IBM gives MIT a supercomputer for computational and systems biology


IBM has awarded a high-performance grid-based computer to MIT's new Computational and Systems Biology Initiative to assist with tackling problems in bioinformatics, genomics, image informatics and structural biology.

The Computational and Systems Biology Initiative (CSBi), established in 2002, is an MIT-wide program linking biology, engineering and computer science in a systems biology approach to the study of cell-to-cell signaling, tissue formation and cancer. CSBi supports and manages research, education and outreach programs as a virtual center with faculty drawn from 10 departments and centers.

The new system, housed in the Artificial Intelligence Laboratory and the W.M. Keck Microscopy facility, will be one of the most powerful computers on campus.

IBM awarded the system to MIT through a grant from its Shared University Research program, which awards computing equipment to colleges and universities around the world to facilitate research projects in areas of mutual interest.

High-performance computers such as those recently acquired by CSBi are playing an increasingly important role in biological research. Bioinformatics, proteomics and pathway modeling are examples of new fields in which computation and numerical modeling join experimental work as important research tools.

Bioinformatics analyzes DNA and protein sequences for important patterns, such as those that differ between normal cells and cancer cells. In proteomics, the properties and functional interactions among large numbers of proteins are explored using automated methods. Proteins carry out the functions of a cell.

CSBi includes the MIT BioMicro Center, which focuses on DNA microarray analysis and molecular bioinformatics. Laboratories working with the center are developing new methods in biological computation, protein arraying, biomolecular electronics and pathway modeling.

These new techniques, which still present challenges for researchers, also allow higher resolutions and a greater fundamental understanding of cells than ever before.

The IBM system, secured through the efforts of Forbes Dewey, professor of mechanical engineering and bioengineering, will be operated by an interdepartmental working group comprising Whitehead Institute investigator Paul T. Matsudaira, professor of biology and biological engineering; Amy E. Keating, assistant professor of biology; and Bruce Tidor, associate professor of bioengineering and computer science and co-chair of CSBi.

The IBM supercomputer will join a second new CSBi high-performance computer now being installed in the BioMicro Center. A faculty team led by CSBi co-chair Peter K. Sorger, associate professor of biology, was recently awarded an NSF grant to install a 128-processor Beowulf Cluster Computer. The Beowulf performs tasks that require large numbers of computations executed in parallel.

Christopher B. Burge, assistant professor of biology, is among the faculty members using the Beowulf for genomics research. The Burge laboratory seeks to understand the rules of RNA splicing specificity. "We're beginning to use a combination of computational and experimental methods to study alternative splicing, a common mechanism of gene regulation in vertebrates," he said.

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A version of this article appeared in MIT Tech Talk on January 29, 2003.


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