A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP

  • NISHIKAWA Yuri
    Faculty of Science and Technology, Keio University
  • OSANA Yasunori
    Graduate School of Science and Technology, Keio University
  • YOSHIMI Masato
    Graduate School of Science and Technology, Keio University
  • IWAOKA Yow
    Graduate School of Science and Technology, Keio University
  • KOJIMA Toshinori
    Faculty of Science and Technology, Keio University
  • FUNAHASHI Akira
    Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency
  • HIROI Noriko
    Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency
  • SHIBATA Yuichiro
    Dept. of Computer and Information Sciences, Nagasaki University
  • IWANAGA Naoki
    Dept. of Computer and Information Sciences, Nagasaki University
  • KITANO Hiroaki
    Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency
  • AMANO Hideharu
    Graduate School of Science and Technology, Keio University

Bibliographic Information

Other Title
  • FPGAを用いた生化学シミュレータReCSiPにおける数値積分機構の性能改善手法(FPGAとその応用及び一般)

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Description

Computational simulation is a highly effective solution for cellular analyses in recent bioinformatics. As the scale of analysis objects are rapidly expanding, however, it is a prime task to develop a simulator with high throughput. ReCSiP, an FPGA-based biochemical simulator, is being exploited for this necessity. Further speed-up of the simulator is enhanced with an improvement of its pipelining efficiency, by a parallel operation of a rate-law solver module and a numerical integration module. This research report discusses the methodology of enhancing the performance of ReCSiP, its implementation and the evaluation result. Speed-up of 1.96x in maximum is achieved with an area increase of 29% compared to the conventional implementation.

Journal

  • Technical report of IEICE. VLD

    Technical report of IEICE. VLD 105 (514), 53-58, 2006-01-11

    The Institute of Electronics, Information and Communication Engineers

Keywords

Details 詳細情報について

  • CRID
    1574231876749104128
  • NII Article ID
    110004071160
  • NII Book ID
    AN10013323
  • Text Lang
    ja
  • Data Source
    • CiNii Articles

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