Performance evaluation of an FPGA-based biochemical simulator ReCSiP

Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Hideharu Amano, Yuichiro Shibata, Naoki Iwanaga

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

ReCSiP is an FPGA-based biochemical simulator to accelerate kinetic simulations of biochemical pathways. Biochemical models are described as a set of ordinary differential equations (ODEs). Each equation in the model is called "rate law function", which represents the velocity of corresponding biochemical reaction mechanism. ReCSiP achieves high-throughput simulation with statically pipelined rate law function modules and numerical integration modules on an FPGA. This paper shows the basic structure of ReCSiP, and results of evaluation in 2 aspects: area and throughput. As the summary of evaluation, 1) about 64% of the total circuit area is occupied by floating-point arithmetic units, and 2) with an XC2VP70, ReCSiP at 90MHz can achieve 20x or more speedup compared to Intel's Pentium4 microprocessor at 3.2GHz.

Original languageEnglish
Title of host publicationProceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL
Pages845-850
Number of pages6
DOIs
Publication statusPublished - 2006 Dec 1
Event2006 International Conference on Field Programmable Logic and Applications, FPL - Madrid, Spain
Duration: 2006 Aug 282006 Aug 30

Publication series

NameProceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL

Other

Other2006 International Conference on Field Programmable Logic and Applications, FPL
CountrySpain
CityMadrid
Period06/8/2806/8/30

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Electrical and Electronic Engineering

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