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Fujitsu Paves the Way for Next-Generation Genomics-Based Drug Design with Bioinformatics

Begins Validation Tests of Its "BioServer," A Massively Parallel Server

Fujitsu Limited

Tokyo, November 05, 2003

Fujitsu Limited today announced that, together with Fujitsu Laboratories Ltd., it has developed a massively parallel simulation server, code-named the "BioServer," that will form the core system for Fujitsu's Genomics-based Drug Design Solutions (*1). The companies also announced that ZOEGENE Corporation (*2), their partner in the biotechnology field, has started validation tests of the BioServer. As an application server specially designed for genomics-based drug design, the BioServer represents a tremendous leap in the effectiveness of genomics-based drug design, enabling greater speed and precision to be applied to the analysis of the structures and functions of proteins, and thereby paving the way towards personalized medicine and the development of novel biopharmaceutical treatments.

With the completion of the full human genome sequence in April of 2003, researchers are now actively engaged in drug design based on genomics information, and are also pursuing personalized medicines that take individual genetic differences into account. Tens of thousands of genes in human DNA control the expression of proteins that do everything from create our internal organs to protect our bodies. Accordingly, with our knowledge of the human genome, an understanding of the proteins created by our genes-the number of protein types, the structure of proteins and their binding habits-will be vitally important to drug design.

Research conducted in a laboratory is mostly done by analysis based on actual experimentation, which entails costly reagents and testing equipment. Applying computer simulation to focus on an area of experimentation prior to the testing phase can save time and money. However, since proteins are large molecules consisting of tens of thousands or even millions of atoms, a staggering amount of computing time is required to calculate their complete structure. This calculation time can be reduced by making partial calculations and simplifying the target molecule, but accuracy and the usefulness of the results are often decreased.

Fujitsu has sought to address these problems through the development of its massively parallel simulator, the BioServer. The BioServer is a new type of application server that is specially designed for genomics-based drug design, combining low power requirements with high-speed processing and high-density mounting. Up to a total of 1,920 CPUs can be assembled in a single rack of the BioServer, with dimensions of approximately 2 feet wide, 3 feet deep and 6.5 feet high. Each of the 1920 processors is simultaneously executing a simulation program that models a protein's structure and binding characteristics. By having each processor operate independently, and in parallel to calculate the model under different conditions, the BioServer is able to quickly produce highly precise simulations.

The individual CPUs in the BioServer are from Fujitsu's FR-V series of embedded processors, which use the Very Long Instruction Word (VLIW) architecture based on the company's supercomputer technology. The power consumption of the CPU, however, is only one-fiftieth of a typical processor used in a PC. The machine runs the axLinux operating system from AXE, Inc.(*3) "In one stroke, the BioServer gives us access to 2000 times the calculating power of the desktop computers we have been using, removing a bottleneck on drug design and making the development of new compounds exceedingly more efficient," said Masayuki Mitsuka, Ph.D., Director of Business Development of ZOEGENE.

BioServer #1, with 1,920 CPUs, is installed at Fujitsu's Internet Data Center, where Fujitsu and ZOEGENE are conducting validation testing. BioServer #2, with 1,280 CPUs, is installed at Fujitsu, where it is slated to be used in aptamer research being conducted as part of a New Energy and Industrial Technology Development Organization (NEDO) bioinformatics development project.

The Genomics-based Drug Design Solution is a systematic compilation of biochemical research, support, software and development technologies built on Fujitsu's 20 years of experience in the field. The design solution consists of a series of genome analysis, protein analysis, and compound design tools that can handle vast quantities of data derived from biological experiments.

The BioServer, as the core system of this solution, overcomes previous difficulties in using a computer to implement an integrated research process flow, and is thereby expected to greatly increase the efficiency of genomics-based drug design.

Fujitsu is committed to using its leadership in IT to help bring about a new era in life sciences and contribute to the development of preventive medicines for a future in which people live happier, healthier lives.

ZOEGENE's Bioinformatics Research System

Hardware:
One BioServer massively parallel simulation server (1,920 CPUs)
Two PRIMEPOWER high-volume processing servers
One ETERNUS network disk array storage system with a capacity of 1.5 TB

Software:
GROMACS (*4) molecular dynamics simulation program
CAChe molecular modeling program (made by Fujitsu)
BioMedCAChe ActiveSite protein modeling program (Fujitsu)
CAChe LocalSCF ultrafast semi-empirical program designed for fast electronic structure calculations of large, complex proteins (Fujitsu) MOPAC general-purpose semi-empirical quantum mechanics program (Fujitsu)
GeneSphereTM-Enterprise gene & protein information analysis tool (Fujitsu).


  • [1] * Genomics-based Drug Design Solution

    A coordinated suite of software, servers, and services to assist drug discovery researchers

  • [2] * ZOEGENE Corporation

    A wholly owned subsidiary of Mitsubishi Chemical that develops and licenses tools for genomics-based drug development.

  • [3] * AXE, Inc.

    Kyoto-based company that develops and markets embedded operating systems for PDAs and other mobile devices. Representative director: Shozo Takeoka.

  • [4] * GROMACS

    A program for calculating molecular dynamics, developed at Groningen University, available under the GNU General Public License, which allows others to revise, redistribute, and sell variations of the software as long as any revisions to the source code are disclosed to the public.

About Fujitsu

Fujitsu is a leading provider of customer-focused IT and communications solutions for the global marketplace. Pace-setting technologies, highly reliable computing and telecommunications platforms, and a worldwide corps of systems and services experts uniquely position Fujitsu to deliver comprehensive solutions that open up infinite possibilities for its customers' success. Headquartered in Tokyo, Fujitsu Limited (TSE:6702) reported consolidated revenues of 4.6 trillion yen (US$38 billion) for the fiscal year ended March 31, 2003.  
For more information, please see: www.fujitsu.com

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Please understand that product prices, specifications and other details are current on the day of issue of the press release, however, may change thereafter without notice.

Date: 05 November, 2003
City: Tokyo
Company: Fujitsu Limited, , , , ,

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