ISU scientists use supercomputer in corn genome project
Date: 9.2.2006
Scientists at Iowa State University will use one of the nation’s 10 most powerful computers to help decipher the corn genome, allowing 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.
Their new $1.25 million IBM BlueGene supercomputer, unveiled Monday, 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.
That gets information much quicker to plant breeders, who can make faster progress in modifying corn plants.
‘‘This is very important because this allows us to modify the corn plant to meet any of our future needs,’’ said Patrick Schnable, an agronomy professor and director of the Center for Plant Genomics at ISU.
Understanding the genome will allow plant biologists to ‘‘build a better corn plant that, for example, produces biodegradable plastic or ethanol or whatever we need to,’’ Schnable said.
‘‘We can make partial assemblies. We can do it every month if we need to, so that the latest data are incorporated and available to plant scientists around the world,’’ Schnable said.
Iowa State is one of four universities working on the corn genome project, which is scheduled to run for three years.
The BlueGene/L computer, contained in two gray boxes about the size of large side-by-side refrigerators, 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.
The supercomputer is housed two blocks from the site where John Atanasoff and Clifford Berry designed the prototype for the world’s first automatic digital computer in 1939. A replica of that machine is on display in the lobby.
"Source":[ http://www.checkbiotech.org/root/index.cfm?fuseaction=news&doc_id=12151&start=1&control=218&page_start=1&page_nr=101&pg=1]
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