Title :
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
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;
Conference_Titel :
Field-Programmable Technology, 2005. Proceedings. 2005 IEEE International Conference on
Conference_Location :
Singapore
Print_ISBN :
0-7803-9407-0
DOI :
10.1109/FPT.2005.1568590
