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SGI Breakthrough Technology Empowers Genome Center Research Around the World
Date:4/30/2008

n use for a year (see separate release December 5, 2007) and purchased through a National Institute of Health (NIH) grant, the SGI(R) Altix(R) 4700 system is assisting TGen researchers in understanding the genomic variation -- a process which requires comparison searches of enormous data sets -- that can be rapidly used for diagnosis and treatment of disease in a manner tailored to individual patients.

Since implementing the SGI system, TGen has observed significant performance gains in analyzing large gene expression datasets on the SGI Altix system.

"On SGI's Altix machines, we have used MPI parallel programming libraries and Intel's icc compiler to parallelize and optimize code, respectively," said TGen Scientific Programmer Waibhav Tembe, Ph.D., who has been actively involved in developing and benchmarking several tools on the SGI Altix systems. "Benchmarks run on Melanoma gene expression dataset consisting of about 8,000 genes from several dozens of samples showed that the analysis time was reduced time of completion from seven days to seven hours and generated several statistically significant gene groups identified that are being investigated further by the life scientists and computational biologists. We are very optimistic that such speed improvements will be critical in expediting translational research and help scientists explore a larger solution space by analyzing larger datasets in the future."

TGen's in-house code harnesses the compute power of the SGI Altix system's global shared memory to search for variations as minute as a change on one protein, trying to determine what effect that has across the entire spectrum of what is being observed.

"The success of TGen scientists to date has come at the sacrifice of time," said Dr. Edward Suh, CIO of TGen. "The 64-bit SGI computing instrument optimizes TGen researchers' ability to meet their data analysis needs efficiently, fostering timely and effective discovery for improved hu
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