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BIOLOGICAL INFORMATICS CONSORTIUM SELECTS UNITED DEVICES GRID MP

United Devices and its Japanese partner, Sumisho Electronics Co, announced the adoption of Grid MP by the Japan Biological Informatics Consortium -- Japan Biological Information Research Center (JBIRC). JBIRC is using Grid MP to configure an intra-organization Grid that utilizes the research center's numerous workstations, implementing this Grid for protein modeling and virtual screening via a Grid-enabled software product developed by JBIRC.

JBIRC is a joint research body made up of the Japan Biological Informatics Consortium (whose members include major food companies, pharmaceutical companies, information device manufacturers) and the Biological Information Research Center. JBIRC has developed an original protein modeling program based on molecular dynamics and an original in-silico screening program based on protein docking simulation. These programs are being made available to JBIRC members and to the general public as an integrated environment under the product name "prestoX."

Traditionally, these types of computationally intense programs have been implemented on high-performance cluster systems owned by JBIRC's computation group. In recent years, other groups within JBIRC including the laboratory group have begun to use such programs as well -- bringing up the issue of how to provide adequate computational resources organization-wide in a cost-effective manner. A Grid MP solution was selected due to its ability to easily deliver such power in a distributed, heterogeneous environment, its proven capacity to scale, and its proven cost-saving benefits.

In addition, because not all users (either JBIRC members or the general public) possess high-performance cluster systems, JBIRC has designed "sievgene," a prestoX medicinal substance-docking tool, to be Grid-enabled. JBIRC recognized the value of developing this tool specifically for Grid use, optimizing its ability to perform in a distributed environment and eliminating the need for additional, costly high-performance equipment.

Stated Yoshifumi Fukunishi, a member of the JBIRC's structural genome analysis group structural information analysis team headed by Haruki Nakamura, "The laboratory group, unlike the computational group, does not need a high performance computational device all the time. But when one is needed, the demand on computational power is enormous. By integrating and making available the computational power of the 100 or so office PCs at the JBIRC using Grid MP, we are able to meet the demand for computational resources without having to acquire a new high-performance cluster. Moreover, it has always been relatively difficult to run software for biotechnology on ordinary personal computers. We have overcome this problem by developing prestoX sievgene to be Grid-enabled."

In a sievgene docking simulation, chemical compound data is divided up into segments for simultaneous processing on the Grid. Because the computation time for the segmented data is relatively short and because the algorithm obtains processing speed on an ordinary PC similar to that of the CPU of a high performance cluster system, sievgene is highly compatible with a PC Grid. JBIRC is thus able to obtain performance levels from its 100 workstations, including even notebook PCs, equivalent to its current high performance cluster.

Added Yoshifumi Fukunishi, "I believe that sievgene, a domestically-developed application with precision unrivaled by any other commercial docking simulation application, would be of special benefit to users besides the JBIRC. And because it supports Grid environments not only on high performance computational devices but also on ordinary PCs, it should be useful to a wide range of users, from drug discovery researchers to structural biology scientists who need three-dimensional analysis of proteins."