SGI breakthrough technology empowers genome centre research around the world

Boston 30 April 2008As scientists seek to accelerate sequencing genomes of varied arrays of organisms from fish parasites to cancer cells in an effort to determine causes and cures of diseases that plague mankind, breakthrough technology from SGI is powering research in genome centres around the world. Leading institutions, including the Translational Genomics Research Institute in Phoenix, Arizona, the Malaysia Genome Institute in Selangor and the China National Human Genome Center in Shanghai, have turned to SGI high-performance computing and storage solutions to create an optimal work flow for faster time to discovery.

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"Exciting combinations of SGI technology enable bioscientists to achieve genome query results faster", stated Deepak Thakkar, Ph.D., Higher Education and Research Segment Manager, SGI. "International genome centres, each with unique computational needs and demands, have turned to SGI for their high performance compute, scalable storage and acceleration technology needs. Whether using an SGI cluster to run many iterations of a search or handling massive data sets on our powerful servers, bioscientists rely on SGI delivering faster time to insight."

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 analyse molecular profile data sets in their search for cancer cures. In use for a year and purchased through a National Institute of Health (NIH) grant, the SGI Altix 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 analysing 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", stated 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 8000 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 analysing 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", stated 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 human health."

The Malaysia Genome Institute (MGI) is a network-based organisation 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 Altix XE 1200 clusters, an SGI Altix 4700 shared memory server and an SGI InfiniteStorage CXFS SAN shared filesystem, which makes the entire work flow transparent to the user regardless of software employed, or stage of the process at which scientists are performing.

"Bioinformatics brings together an avalanche of systematic biological data with the analytic theory and practical tools of mathematics and computer science", stated 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."

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 China area. To study the parasite evolution, improve disease diagnosis in the very early stages, and develop more effective drugs to treat disease, bioscientists at the China National Human Genome Center (CHGC) in Shanghai are using a combination of SGI Reconfigurable Application-Specific Computing (RASC) technology, an accelerated version of BLAST-n - Basic Local Alignment Search Tool for nucleotides - software developed by Mitrionics, and the SGI Altix server platform.

CHGC implemented blood fluke genomics sequencing using the SGI RASC Appliance for Bioinformatics and SGI InfiniteStorage 350 storage solution. CHGC bioscientists achieve fast query times with the SGI InfiniteStorage 350, which ensures the data generated by the CHGC research, reaching hundreds of gigabytes in size, is both protected and available to maximize analysis.

"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", stated 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.

More SGI news is available in the VMW April 2008 article At Technische Universität Dresden, SGI Altix accelerates three months of research into a single day.


Leslie Versweyveld

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