A combining technique of rate law functions for a cost-effective reconfigurable biological simulator

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

doi:10.1109/FPL.2007.4380774

A combining technique of rate law functions for a cost-effective reconfigurable biological simulator

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

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

2 Citations (Scopus)

Abstract

In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources are essential. This paper proposes a method which combines common terms in rate law functions appeared in biochemical models and generates a shared hardware module used for numerical integration. In this approach, two functions are combined in a tree structure level, followed by pipeline scheduling and arithmetic module binding. The evaluation result reveals that this approach reduces hardware resources by 31.4 % on average at the cost of 14.4 % throughput degradation.

Original language	English
Title of host publication	Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
Pages	808-811
Number of pages	4
DOIs	https://doi.org/10.1109/FPL.2007.4380774
Publication status	Published - 2007
Event	2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands Duration: 2007 Aug 27 → 2007 Aug 29

Publication series

Name	Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL

Other

Other	2007 International Conference on Field Programmable Logic and Applications, FPL
Country/Territory	Netherlands
City	Amsterdam
Period	07/8/27 → 07/8/29

ASJC Scopus subject areas

Computer Science Applications
Electrical and Electronic Engineering

Access to Document

10.1109/FPL.2007.4380774

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Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Hiroaki Kitano, K., & Kiyoshi Oguri, O. (2007). A combining technique of rate law functions for a cost-effective reconfigurable biological simulator. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL (pp. 808-811). [4380774] (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2007.4380774

A combining technique of rate law functions for a cost-effective reconfigurable biological simulator. / Yamada, Hideki; Iwanaga, Naoki; Shibata, Yuichiro; Osana, Yasunori; Yoshimi, Masato; Iwaoka, Yow; Nishikawa, Yuri; Kojima, Toshinori; Amano, Hideharu ; Funahashi, Akira; Hiroi, Noriko; Hiroaki Kitano, Kitano; Kiyoshi Oguri, Oguri.

Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 808-811 4380774 (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

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

Yamada, H, Iwanaga, N, Shibata, Y, Osana, Y, Yoshimi, M, Iwaoka, Y, Nishikawa, Y, Kojima, T, Amano, H , Funahashi, A, Hiroi, N, Hiroaki Kitano, K & Kiyoshi Oguri, O 2007, A combining technique of rate law functions for a cost-effective reconfigurable biological simulator. in Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL., 4380774, Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL, pp. 808-811, 2007 International Conference on Field Programmable Logic and Applications, FPL, Amsterdam, Netherlands, 07/8/27. https://doi.org/10.1109/FPL.2007.4380774

Yamada H, Iwanaga N, Shibata Y, Osana Y, Yoshimi M, Iwaoka Y et al. A combining technique of rate law functions for a cost-effective reconfigurable biological simulator. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 808-811. 4380774. (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2007.4380774

Yamada, Hideki ; Iwanaga, Naoki ; Shibata, Yuichiro ; Osana, Yasunori ; Yoshimi, Masato ; Iwaoka, Yow ; Nishikawa, Yuri ; Kojima, Toshinori ; Amano, Hideharu ; Funahashi, Akira ; Hiroi, Noriko ; Hiroaki Kitano, Kitano ; Kiyoshi Oguri, Oguri. / A combining technique of rate law functions for a cost-effective reconfigurable biological simulator. Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. pp. 808-811 (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

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AB - In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources are essential. This paper proposes a method which combines common terms in rate law functions appeared in biochemical models and generates a shared hardware module used for numerical integration. In this approach, two functions are combined in a tree structure level, followed by pipeline scheduling and arithmetic module binding. The evaluation result reveals that this approach reduces hardware resources by 31.4 % on average at the cost of 14.4 % throughput degradation.

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A combining technique of rate law functions for a cost-effective reconfigurable biological simulator

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