SGI News
SGI Breakthrough Technology Empowers Genome Center Research Around the World
"Exciting combinations of SGI technology enable bioscientists to achieve genome query results faster," said
The Translational Genomics Research Institute
Discovering the differences and changes within the genome that trigger disease is a priority for The Translational Genomics Research Institute (TGen). TGen deploys technology from SGI to more quickly and efficiently analyze molecular profile data sets in their search for cancer cures. In use for a year (see separate release
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.
Malaysia Genome Institute
The Malaysia Genome Institute (MGI) is a network-based organization with international ties carrying out discovery research on tropical bioresources through projects in genome sequencing, comparative and functional genomics, and structural biology. Several major research projects are currently underway at MGI. For example, the Microbial Genomics Research for Gene and Natural Product Discovery project is focusing on two model organisms, Burkholderia pseudomallei, a locally important soil pathogen and Eimeria tenella, a local avian protozoan. The project will harness the SGI solution to dissect the organisms' genomes to gain new insights on virulence, antibiotic resistance, host specificity and infectivity.
Installed in July, 2007, MGI uses a hybrid computing solution that consists of SGI(R) Altix(R) XE 1200 clusters, an SGI(R) Altix(R) 4700 shared memory server and an SGI(R) InfiniteStorage CXFS(TM) SAN shared filesystem, which makes the entire workflow transparent to the user regardless of software employed, or stage of the process at which scientists are performing. (See separate release
"Bioinformatics brings together an avalanche of systematic biological data with the analytic theory and practical tools of mathematics and computer science," said Mohd Noor Mat Isa, Laboratory Manager, Malaysia Genome Institute. "SGI delivers flexible computing with a hybrid architecture that integrates high-throughput, high-performance and FPGA-based solutions for all of our bioinformatics applications — a solution that seamlessly runs applications in the environment best suited for optimal performance."
China National Human Genome Center
Schistosoma japonicum or blood fluke — one of the major infectious parasites to a wide range of hosts including primates, rodents, carnivores, and humans — has evolved for thousands of years. In the past few years the Schistosoma japonicum has been found in some lakes and rivers in the east and south
CHGC implemented blood fluke genomics sequencing using the SGI RASC Appliance for Bioinformatics and SGI InfiniteStorage 350 storage solution (See separate release
"Shortened time to results is critical to our success. With the blood fluke genome research, we have 300 million base pairs to study, and have 6-7 times more calculations in each step. The large shared memory and ease-of-use with SGI RASC and SGI server and storage systems enables our scientists to focus on achieving results faster and not spending valuable time on computer science," said Dr. Zhou, Deputy Director of Bioinformatics Department, CHGC.
The Mitrion accelerated BLAST-n running on the SGI RASC Appliance for Bioinformatics runs large queries up to 19 times faster than a single-core cluster powered by AMD Opteron 8820 SE processors, and production runs of thousands of smaller queries by up to 60 times faster.
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SGI (Nasdaq: SGIC) is a leader in high-performance computing. SGI delivers a complete range of high-performance server, visualization and storage solutions along with industry-leading professional services and support that enable its customers to overcome the challenges of complex data-intensive workflows and accelerate breakthrough discoveries, innovation and information transformation. SGI helps customers solve significant challenges whether it's enhancing the quality of life through drug research, designing and manufacturing safer and more efficient cars and airplanes, studying global climate change, providing technologies for homeland security and defense, or helping enterprises manage large data. With offices worldwide, the company is headquartered in
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