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Kyoto University Purchases 768-CPU SGI Origin 3800 Supercomputer to Back KEGG Database


  The Institute for Chemical Research (ICR) at Kyoto University, home of the Kyoto Encyclopedia of Genes and Genomes (KEGG), has purchased a 768-CPU parallel supercomputing system from SGI that it said is one of the biggest supercomputing systems in Japan.

Minoru Kanehisa, a professor at the ICR Bioinformatics Center, said the institute chose the SGI Origin 3800 system largely to support the KEGG system. “The data objects in KEGG are huge graphs encompassing the entire gene universe, representing relationships among all known genes,” he said. “We needed not only a massively parallel computing capability but also a large shared memory space.” The institute will also use the system to support its work in bioinformatics and computational chemistry research.

This fall, SGI will install two Origin 3800 systems, with 512 CPUs dedicated to computational chemistry and 256 CPUs for computational biology. The company is also delivering an Onyx 3400 visualization system with 32 CPUs and a TP9400 35 TB storage system. Operations are expected to begin in January 2002.

The deal is the latest step in a decade-long relationship between SGI and the ICR. The institute’s existing SGI equipment included a 128-CPU SGI Origin 2000, a 4-CPU Origin 2000, a 4-CPU Onyx IR, a 32-CPU PowerChallenge, and a 72-CPU SGI 1450. The new agreement will replace all the servers except the SGI 1450.

SGI also played a role in the launch of the ICR’s GenomeNet Database Service (, which includes the suite of KEGG databases as well as tools for retrieval and sequence interpretation. SGI spokeswoman Tomoko Nakanishi said the company is responsible for the general operation and management of the service, including its anonymous FTP service, and is also involved in the development of some of the homology search tools.

SGI said it intends to extend its relationship with ICR even further by funding an upcoming three-year professor position and training course within ICR’s Bioinformatics Laboratory. Nakanishi said the training course would be designed for general users of the SGI system at the ICR and would offer training in UNIX, bioinformatics applications, and general operation of the system.

Continued support of bioinformatics in Japan is part of SGI’s strategy to grow its share of the Japanese UNIX server market. The company currently ranks fifth, with 9.8 percent of the market, behind Sun (30.1 percent), Hewlett-Packard (27.7 percent), IBM (12.1 percent), and Fujitsu (10.5 percent). However, this represents 123.6 percent growth over the company’s 5.1 percent share of the market for the first half of 2000.

SGI is currently finalizing several other key deals in Asia, including an agreement with the National Center for Gene Research of Shanghai Life Science for a 32-processor SGI Origin 3800 system that will be used for the genetic analysis of rice grain and a strategic alliance with NEC that may involve the development of software related to genome research and biotechnology.

— BT

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