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IBM and DOE pool supercomputing talents to examine disease

Massive computing power and biology are coming together in a big way through a cooperative research and development agreement between IBM and the U.S. Department of Energy's Oak Ridge National Laboratory



This image illustrates how computational biology techniques can be used to help understand the characteristics needed to design effective drug compounds to fight disease.

November 12—At the heart of the agreement is IBM's Blue Gene research project, which combines advanced protein science with IBM's next-generation cellular architecture supercomputer design.

Unlike today's computers, cellular servers will run on chips containing "cells," which are processors that contain memory and communications circuits. Cellular architecture will help scale computer performance from teraflops (1 trillion calculations per second) to petaflops (1,000 trillion calculations per second).

"Our collaboration with Oak Ridge National Laboratory is vital to IBM's work to extend the boundaries for applications of large-scale computing, focusing on the combination of IBM and ORNL's deep scientific capabilities," said David McQueeney, vice president of Emerging Business for IBM Research. "Together we have built a common roadmap for an ambitious multi-year evolution of the simulation and modeling of many complex systems. We are confident that we will break new ground in several domains, including life sciences."

Super computing power has major implications for gaining a better understanding of gene sequences and how folding of proteins relates to diseases.

"Proteins control all processes occurring in the cells of the body," said Joe Jasinski, manager, Computational Biology Center for IBM Research. "These proteins are made up of a vast array of different combinations of amino acids that fold and bend into very complex three-dimensional shapes that determine the exact function of each protein."

"If the shape of these proteins changes because of some environmental, physical or biological factor, the protein may turn from being beneficial to one that causes specific diseases."

IBM and ORNL hope to use this enormous computing power to explore numerous other areas as well. Because the project is a collaboration of ORNL's Life Sciences and Computer Science and Mathematics divisions and IBM, it draws from a sizeable pool of resources. The project also provides ORNL with new challenges.

"The complexity of the protein folding problem, nanoscale science, and climate dynamics will require computational resources at a scale not yet achieved by any scientific application," said Thomas Zacharia, director of ORNL's Computer Science and Mathematics Division. "This is an exciting next step in ORNL's history of evaluating new computational architectures and pushing the computational science envelope."

Indeed, before it is possible to solve these scientific problems, scientists will have to devise methods to run applications that use tens of thousands of processors in IBM's Blue Gene supercomputer. Each processor forms a cell with memory, communication, and input/output built in. This approach departs from past designs and offers a glimpse of what's to come in high-performance computing.—by Ron Walli

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