A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA

Author

Yoshimi, Masato ; Nishikawa, Yuri ; Kojima, Toshlinori ; Osana, Yasunori ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yoshitaka ; Yamada, Hiroyoshi ; Kitano, Hiroaki ; Amano, Hideharu

Author_Institution

Keio Univ., Yokohama

fYear

2007

fDate

12-14 Dec. 2007

Firstpage

193

Lastpage

200

Abstract

This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the next reaction method, known for its large number of calculation involved. The procedure is divided into several subdivisions which will be implemented as independent modules, and they are connected with configurable interconnection networks so as to provide high throughput. By performing a multi-threading simulation, 3.6 times speedup was obtained compared with an execution on general purpose processors.

Keywords

biochemistry; biology computing; field programmable gate arrays; stochastic processes; configurable interconnection networks; field programmable gate arrays; multithreading simulation; network-based FPGA implementation; network-based stochastic biochemical simulator; next reaction method; stochastic simulation algorithm; Algorithm design and analysis; Bioinformatics; Circuit simulation; Computational modeling; Computer networks; Computer science; Field programmable gate arrays; Stochastic processes; Stochastic systems; Yarn;

fLanguage

English

Publisher

ieee

Conference_Titel

Field-Programmable Technology, 2007. ICFPT 2007. International Conference on

Conference_Location

Kitakyushu

Print_ISBN

978-1-4244-1472-7

Electronic_ISBN

978-1-4244-1472-7

Type

conf

DOI

10.1109/FPT.2007.4439249

Filename

4439249