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Southwest Foundation for Biomedical Research to expand one of the world’s largest computer clusters for exploring human genes

The “computer ranch” at the Southwest Foundation for Biomedical Research (SFBR) will more than double in size this summer, thanks to a $2 million federal grant that will create new jobs as it speeds the pace of discovery at the Foundation’s AT&T Genomics Computing Center.

The grant will fund the manufacture and installation of 5,004 more linked processors for the computing center. That will give the Foundation a total of 8,004 linked computers that can work in tandem to process the billions of calculations required for complex genetic analyses. Installation of the processors should begin in August and be completed by the middle of September.

The investment will more than double the computing power of the ranch and provide a 20-fold increase in data storage capacity, said John Blangero, Ph.D., a statistical geneticist and director of the computing center.

Until recently, cost and technological limits meant that scientists had to focus any study on a narrow segment of the genome. The field is advancing rapidly, though, and soon computational geneticists will be able to undertake complete genome sequencing of individual subjects in their studies, said Blangero.

“Our expansion will provide us with sufficient computational firepower to handle the coming flood of whole human genome sequencing, which will become cost-effective in the next one to two years,” Blangero said. “This investment will keep the Foundation at the forefront of the expanding genetic frontier.”

Funding for the expansion comes through the American Recovery and Reinvestment Act, part of the economic stimulus package approved by Congress in 2009. It provided money to the National Center for Research Resources, a part of the National Institutes of Health (NIH), to make awards for scientific equipment investments at research institutions across the country. The Foundation’s grant application got a perfect score in the competitive review process, which considered both the equipment’s effect on scientific research and its impact on job creation.

The Foundation will add one systems analyst position because of the computer expansion, Blangero said. M&A Technology Inc. of Carrollton, Texas, which will manufacture, install and maintain the specialized processors, will add one or possibly two new positions because of its contract with the Foundation, said Senior Vice President Val Overbey Sr.

M&A Technology has sales and service operations in San Antonio. Formed in 1984, it has been the Foundation’s partner since 2002 in designing, assembling and maintaining the computer ranch.

The computers support $110 million worth of NIH grants, giving the Foundation a compelling case in favor of the additional federal investment, said Blangero. “The decision was made that giving us $2 million to support our work was a good idea,” he said. “We also showed that we had a need for expansion because of the cutting-edge computational activities that we are engaged in.”

Foundation scientists are directing or supporting a number of studies that employ extended family pedigrees to track down the genetic basis of chronic complex diseases. These include the San Antonio Family Heart Study, begun at the Foundation in 1991, which has involved 1,400 Mexican Americans from 40 San Antonio-area families in the search for genes that influence heart disease, diabetes and obesity. The genetic data collected in that study has given rise to several others, including studies now looking at the genetic determinants of brain structure and the genetic basis of psychiatric illnesses.