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 proceedingConference 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 languageEnglish
Title of host publicationProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
Pages808-811
Number of pages4
DOIs
Publication statusPublished - 2007
Event2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands
Duration: 2007 Aug 272007 Aug 29

Other

Other2007 International Conference on Field Programmable Logic and Applications, FPL
CountryNetherlands
CityAmsterdam
Period07/8/2707/8/29

Fingerprint

Simulators
Hardware
Field programmable gate arrays (FPGA)
Costs
Pipelines
Scheduling
Throughput
Degradation

ASJC Scopus subject areas

  • Computer Science Applications
  • Electrical and Electronic Engineering

Cite this

Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., ... 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] 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.

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