The design of scalable stochastic biochemical simulator on FPGA

Author

Yoshimi, Masato ; Osana, Yasunori ; Iwaoka, Yow ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Iwanaga, Naoki ; Kitano, Hiroaki ; Amano, Hideharu

Author_Institution

Dept. of Comput. Sci., Keio Univ., Yokohama

fYear

2005

fDate

11-14 Dec. 2005

Firstpage

339

Lastpage

340

Abstract

Biochemical simulations including whole-cell models require high performance computing systems. Reconfigurable systems are expected to be an alternative solution for conventional methods by PC clusters or vector computers. This paper shows the implementation of a stochastic biochemical simulation algorithm called Next Reaction Method for Virtex-II PRO. As the result of benchmarking with a small reaction system, the FPGA-based simulator outperforms the software implementation on Xeon 2.40 GHz by 17.1 times

Keywords

Monte Carlo methods; biocomputing; field programmable gate arrays; reconfigurable architectures; stochastic processes; 2.40 GHz; PC clusters; Virtex-II PRO; field programmable gate array; high performance computing systems; next reaction method; reconfigurable systems; stochastic biochemical simulator; vector computers; Arithmetic; Binary trees; Computational modeling; Computer science; Computer simulation; Field programmable gate arrays; High performance computing; Stochastic processes; Stochastic systems; Switches;

fLanguage

English

Publisher

ieee

Conference_Titel

Field-Programmable Technology, 2005. Proceedings. 2005 IEEE International Conference on

Conference_Location

Singapore

Print_ISBN

0-7803-9407-0

Type

conf

DOI

10.1109/FPT.2005.1568590

Filename

1568590