Title :
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
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;
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
DOI :
10.1109/FPT.2007.4439249
