University of Pittsburgh’s 125-node Apple Xserve G5 Cluster solves human genetics puzzles

“Every week in the CBS network’s new hit series Numb3rs, an FBI agent relies on his math genius brother to find patterns and equations that help to solve crimes. With its new Apple Xserve G5 computing cluster, the University of Pittsburgh’s Graduate School of Public Health (GSPH) is solving double-helix puzzles in human genetics every day — and faster than a speeding FBI-issue bullet,” The University of Pittsburgh Medical Center (UPMC) reports.

“Using the school’s newly installed 125-node Xserve cluster, more than 30 investigators and scientific teams, engaged in more than 120 complex research projects have all the computing power they could ask for, according to M. Michael Barmada, Ph.D., associate professor in the department of human genetics at GSPH. Paid for with a shared resource grant from the National Institutes of Health, the human genetics computing cluster is among the fastest at an academic medical center in the United States,” UPMC reports. “‘Our division of statistical genetics is looking for genes that influence diseases,’ explained Dr. Barmada, whose research focuses on the genetic epidemiology of common yet complex disorders such as diabetes and inflammatory bowel disease. ‘In a sense, we’re gene hunters.'”

UPMC reports, “Dr. Barmada and his colleagues are using their new computing power — dubbed locally as the Gattaca Cluster for the 1997 feature film — to analyze data involving the many genes that lead to variations in human traits, from those that regulate differences in height and bone density to those that influence susceptibility to disease. ‘With older computers, these complex calculations can take weeks,’ he said. ‘Insights into the factors that contribute to diseases give us targets for effective therapy. The new Gattaca Cluster is a terrific tool to help the discovery process.’ Future plans exist to extend Gattaca’s workload even more by analyzing data from microarrays and large SNP-chip studies, which can involve as many as 100,000 markers. ‘This will greatly increase the number of computations required for a genetics project, but Gattaca has the horsepower and storage capacity to handle whatever we throw at it,’ said Dr. Barmada.”

Full article here.

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