An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems

Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Yuri Nishikawa; Toshinori Kojima; Yuichiro Shibata; Naoki Iwanaga; Akira Funahashi; Noriko Hiroi; Hiroaki Kitano; Hideharu Amano

doi:10.1109/FPL.2006.311218

An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems

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

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

6 Citations (Scopus)

Abstract

Stochastic simulation of biochemical systems has become one of major approaches to study life processes as system, yet is a computational challenge to run the simulation due to its vast calculation cost. This paper shows the implementation and evaluation of a stochastic simulation algorithm (SSA) called "First Reaction Method" on an FPGA-based biochemical simulator. It achieves high throughput by (1) consecutively throwing data into deeply-pipelined floating point arithmetic units, and (2) by distruibuting multiple simulators for parallel execution. As the result of evaluation on an FPGA-based simulation platform called ReC-SiP2, the simulator outperforms execution on Xeon 2.80 GHz by approximately 80 times, even with large-scale biochemical systems.

Original language	English
Title of host publication	Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL
Pages	227-232
Number of pages	6
DOIs	https://doi.org/10.1109/FPL.2006.311218
Publication status	Published - 2006 Dec 1
Event	2006 International Conference on Field Programmable Logic and Applications, FPL - Madrid, Spain Duration: 2006 Aug 28 → 2006 Aug 30

Publication series

Name	Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL

Other

Other	2006 International Conference on Field Programmable Logic and Applications, FPL
Country/Territory	Spain
City	Madrid
Period	06/8/28 → 06/8/30

ASJC Scopus subject areas

Computational Theory and Mathematics
Electrical and Electronic Engineering

Access to Document

10.1109/FPL.2006.311218

Cite this

Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., & Amano, H. (2006). An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. In Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL (pp. 227-232). Article 4100980 (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2006.311218

An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. / Yoshimi, Masato; Osana, Yasunori; Iwaoka, Yow et al.
Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. 2006. p. 227-232 4100980 (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Yoshimi, M, Osana, Y, Iwaoka, Y, Nishikawa, Y, Kojima, T, Shibata, Y, Iwanaga, N, Funahashi, A, Hiroi, N, Kitano, H & Amano, H 2006, An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. in Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL., 4100980, Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL, pp. 227-232, 2006 International Conference on Field Programmable Logic and Applications, FPL, Madrid, Spain, 06/8/28. https://doi.org/10.1109/FPL.2006.311218

Yoshimi M, Osana Y, Iwaoka Y, Nishikawa Y, Kojima T, Shibata Y et al. An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems. In Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. 2006. p. 227-232. 4100980. (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL). doi: 10.1109/FPL.2006.311218

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AU - Shibata, Yuichiro

AU - Iwanaga, Naoki

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AU - Kitano, Hiroaki

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AB - Stochastic simulation of biochemical systems has become one of major approaches to study life processes as system, yet is a computational challenge to run the simulation due to its vast calculation cost. This paper shows the implementation and evaluation of a stochastic simulation algorithm (SSA) called "First Reaction Method" on an FPGA-based biochemical simulator. It achieves high throughput by (1) consecutively throwing data into deeply-pipelined floating point arithmetic units, and (2) by distruibuting multiple simulators for parallel execution. As the result of evaluation on an FPGA-based simulation platform called ReC-SiP2, the simulator outperforms execution on Xeon 2.80 GHz by approximately 80 times, even with large-scale biochemical systems.

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An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems

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