Computer center gets $8.5 million

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Understanding how a cell works is important for medical research, but watching one under a microscope doesn't reveal its tiny secrets.

Computer models of cells that react like real ones can, however, provide "the holy grail" of cellular research.

But such cell models require behemoth supercomputing systems that use many thousands of processors to do trillions and even quadrillions of calculations per second for a month or longer.

That's why the National Institutes of Health has awarded the Pittsburgh Supercomputing Center $8.5 million to continue building computer models of cells, among other biomedical projects.

The NIH grant renews funding for five years for the center's newly named National Resource for Biomedical Supercomputing.

It will use the money to continue producing supercomputer models for biomedical research and programs for training and education. The award also will support creation of three-dimensional cellular modeling, large-scale visualization and analysis, and computerization to understand structural biology.

In operation since 1987, the center is a forerunner in use and development of supercomputers. Its 10 teraflop Cray XT3 consists of 2,090 processors and has a peak performance of nearly 10 trillion calculations per second. Applications include nanotechnology, turbulence, protein dynamics leading to new therapeutic drugs, modeling of earthquake soil vibrations and severe storm forecasting.

Among other computer resources at the center, its Hewlett Packard GS1280 AlphaServers, dubbed Jonas and Rachel, will be used to do biomedical and engineering research.

Three-dimensional cellular modeling involves building realistic versions of cells and parts of cells and populating them with proteins, enzymes and other biochemicals to see what happens inside the cells.

One ongoing experiment is designed to show neurotransmitters between nerves and muscle cells and how nerves make muscles move.

"We can put components into a 3-D model and predict how it works in disease," said Joel Stiles, the biomedical program's science director. "But it needs a lot of software."

Dr. Stiles also is a medical doctor and computational physiologist with faculty appointments at Carnegie Mellon University and the University of Pittsburgh.

Other biomedical projects include processing information gathered from medical scans, imaging devices and microscopes to figure out what's happening.

Researchers also will use the supercomputers to study the molecular structure of proteins, nucleic acids and combinations of the two, and how they function. The research will be used to design better drugs by explaining molecules, atoms and the making and breaking of bonds in chemical reactions.

Scientists know what happens when something is added to or subtracted from a cell, but the mystery is why it happens. Supercomputer modeling will help explain the cellular processes that produce predictable results.

"The union of large-scale biology and computing will help us understand that big question," Dr. Stiles said.

Once those questions are answered, supercomputers can help explain how larger organisms and eventually bodies work.

"I hope in the future someday we can make real predictions by gathering information about a patient to determine how that person will respond to drugs or how gene introduction will affect that particular patient," Dr. Stiles said.

The state of biomedical supercomputing today is analogous to where weather prediction was 30 years ago.

"They can predict where hurricanes will hit and the force with which it will hit," he said. "The reason is the coupling between real data they capture and feed daily into a supercomputer to create a model of climate."

Once developed, these systems will have "a giant impact on our lives," Dr. Stiles said.

"It will be a real valuable prediction of how we will respond to treatment," he said. "It will be the holy grail" of predicting reactions in individuals.

The center's biomedical program was one of the first in the nation outside of the National Institutes of Health.

Over the years, more than 3,200 researchers have received biomedical training at the supercomputing center, which has supported more than 1,000 biomedical research projects involving more than 2,500 researchers from 218 research institutions in 48 states.

The $8.5 million grant allows such research to continue.

"The potential is enormous in all these different problems," Dr. Stiles said. "The payoff for every person will be huge."


David Templeton can be reached at dtempleton@post-gazette.com or 412-263-1578.


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