Iowa State University supercomputer to help decipher corn genome

By David Pitt
AMES, Iowa – Scientists at Iowa State University are using one of the nation's 10 most powerful computers to help decipher the corn genome, a project that could allow them to expand the plant's uses in plastics, fuel and fiber.
To determine how a corn genome – the basic genetic structure of the plant – is put together, scientists must assemble more than 60 million bits of genetic material.
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Scientists are planning to use the $1.25 million IBM BlueGene supercomputer, unveiled Monday, which has the equivalent processing power of more than 2,000 home computers and a storage capacity more than 1,000 times greater. It performs as many as 5.7 trillion calculations per second, said Srinivas Aluru, professor of electrical and computer engineering.
The computer's speed enables scientists to shorten the time of processing data that would have previously taken two to three months to just days, Aluru said.

Understanding the genome will allow plant biologists to “build a better corn plant that, for example, produces biodegradable plastic or ethanol,” said Patrick Schnable, an agronomy professor and director of the Center for Plant Genomics at Iowa State University.
Iowa State is one of four universities working on the corn genome project, which is scheduled take about three years.

The BlueGene/L computer is the 73rd most powerful supercomputer in the world, according to a list compiled by scientists at the University of Mannheim in Germany, the University of Tennessee and the Lawrence Berkeley National Laboratory.
It was financed with a $600,000 grant from the National Science Foundation and $650,000 from the university.

Besides the corn genome project, scientists hope to use the supercomputer to help understand protein networks in organisms, which can lead to breakthroughs in disease research.
Such networks can involve 30,000 proteins interacting with each other, too many calculations for the typical computer to perform in adequate time, said Bob Jernigan, professor of biochemistry and biophysics.

“It's the unavailability of computers of this magnitude that limits many projects in engineering and computer science. This can have an important influence on all kinds of research,” he said.

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