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Japan institute selects HPC system to advance genomics research

The Institute for Chemical Research at Kyoto University, Japan, is using an SGI HPC system to advance genomics research. Once in place, the HPC system is expected to consist of SGI UV 1000 systems operating at 32.6 teraflops and delivering up to 6.6x performance increase over the previous system.

The Institute for Chemical Research, founded in 1926 and celebrating its 85th anniversary in 2011, was the first research institute established at Kyoto University. The Institute’s founding vision is to 'excel in the investigation of basic principles of chemistry and their applications'.

'Our research laboratory developed the Kyoto Encyclopedia of Genes and Genomes ('KEGG'), an integrated biosystems database, which has been providing services to researchers around the world as part of GenomeNet,' said Minoru Kanehisa, professor and director of the Bioinformatics Center, Institute for Chemical Research at Kyoto University. 'Adopting the SGI UV 1000 for GenomeNet calculations will dramatically reduce processing time to provide users with the latest data as quickly as possible, and we look forward to taking full advantage of the large amount of genomic information generated by next-generation sequencers as a center for shared usage and joint research.'

The new solution, selected to replace another HPC system in place at the Institute, was configured with more than 3,072 cores of Intel Xeon processor E7 series. It will contain 48TB of total memory and include 840TB of total storage. The HPC system being supplied by SGI consists of two servers, one for computational chemistry and one for 'GenomeNet' calculations.

The computational chemistry server consists of two nodes with 512 cores and 8TB of shared memory. Applications such as quantum chemistry and molecular dynamics will be utilised on the UV 1000, enabling users to run Gaussian, CASTEP, Discover and other programs to examine molecular structures and their specifications and characteristics. The 'GenomeNet' calculation server also consists of two nodes with 1024 cores and 16TB of shared memory. 'GenomeNet' is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University under the leadership of Professor Minoru Kanehisa as part of the university’s research projects.

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