The design of scalable stochastic biochemical simulator on FPGA

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

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

6 Citations (Scopus)

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 2.40GHz by 17.1 times.

Original languageEnglish
Title of host publicationProceedings - 2005 IEEE International Conference on Field Programmable Technology
Pages339-340
Number of pages2
Volume2005
DOIs
Publication statusPublished - 2005
Event2005 IEEE International Conference on Field Programmable Technology - , Singapore
Duration: 2005 Dec 112005 Dec 14

Other

Other2005 IEEE International Conference on Field Programmable Technology
CountrySingapore
Period05/12/1105/12/14

Fingerprint

Benchmarking
Field programmable gate arrays (FPGA)
Simulators

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Yoshimi, M., Osana, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., ... Amano, H. (2005). The design of scalable stochastic biochemical simulator on FPGA. In Proceedings - 2005 IEEE International Conference on Field Programmable Technology (Vol. 2005, pp. 339-340). [1568590] https://doi.org/10.1109/FPT.2005.1568590

The design of scalable stochastic biochemical simulator on FPGA. / Yoshimi, Masato; Osana, Yasunori; Iwaoka, Yow; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Iwanaga, Naoki; Kitano, Hiroaki; Amano, Hideharu.

Proceedings - 2005 IEEE International Conference on Field Programmable Technology. Vol. 2005 2005. p. 339-340 1568590.

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

Yoshimi, M, Osana, Y, Iwaoka, Y, Funahashi, A, Hiroi, N, Shibata, Y, Iwanaga, N, Kitano, H & Amano, H 2005, The design of scalable stochastic biochemical simulator on FPGA. in Proceedings - 2005 IEEE International Conference on Field Programmable Technology. vol. 2005, 1568590, pp. 339-340, 2005 IEEE International Conference on Field Programmable Technology, Singapore, 05/12/11. https://doi.org/10.1109/FPT.2005.1568590
Yoshimi M, Osana Y, Iwaoka Y, Funahashi A, Hiroi N, Shibata Y et al. The design of scalable stochastic biochemical simulator on FPGA. In Proceedings - 2005 IEEE International Conference on Field Programmable Technology. Vol. 2005. 2005. p. 339-340. 1568590 https://doi.org/10.1109/FPT.2005.1568590
Yoshimi, Masato ; Osana, Yasunori ; Iwaoka, Yow ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Iwanaga, Naoki ; Kitano, Hiroaki ; Amano, Hideharu. / The design of scalable stochastic biochemical simulator on FPGA. Proceedings - 2005 IEEE International Conference on Field Programmable Technology. Vol. 2005 2005. pp. 339-340
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