A framework for ODE-based multimodel biochemical simulations on an FPGA

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

doi:10.1109/FPL.2005.1515788

A framework for ODE-based multimodel biochemical simulations on an FPGA

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

研究成果: Conference contribution

3 被引用数 (Scopus)

抄録

Today, mathematical modeling and simulation of biochemical pathways take a major role in biological researches. However, modern microprocessors cannot provide enough throughput to explore the large parameter space of target pathways. To address this problem, ReCSiP (a ReConfigurable Cell Simulation Platform), an FPGA-based biochemical simulator is proposed. It's an ODE-based simulator, which solves the rate-law functions. The framework proposed in this paper, enables to simulate pathways consisting many different types of chemical reactions by connecting the rate-law modules (solvers) on an FPGA. It provides the solver-to-solver communication mechanism on an FPGA and automatic configuration software to generate the circuit.

本文言語	English
ホスト出版物のタイトル	Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
ページ	574-577
ページ数	4
DOI	https://doi.org/10.1109/FPL.2005.1515788
出版ステータス	Published - 2005 12 1
イベント	2005 International Conference on Field Programmable Logic and Applications, FPL - Tampere, Finland 継続期間: 2005 8 24 → 2005 8 26

出版物シリーズ

名前	Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
巻	2005

Other

Other	2005 International Conference on Field Programmable Logic and Applications, FPL
国/地域	Finland
City	Tampere
Period	05/8/24 → 05/8/26

ASJC Scopus subject areas

工学（全般）

文献へのアクセス

10.1109/FPL.2005.1515788

他のファイルとリンク

引用スタイル

Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., & Amano, H. (2005). A framework for ODE-based multimodel biochemical simulations on an FPGA. In Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL (pp. 574-577). [1515788] (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; Vol. 2005). https://doi.org/10.1109/FPL.2005.1515788

A framework for ODE-based multimodel biochemical simulations on an FPGA. / Osana, Yasunori; Fukushima, Tomonori; Yoshimi, Masato; Iwaoka, Yow; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Iwanaga, Naoki; Kitano, Hiroaki; Amano, Hideharu.

Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. 2005. p. 574-577 1515788 (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; Vol. 2005).

研究成果: Conference contribution

Osana, Y, Fukushima, T, Yoshimi, M, Iwaoka, Y, Funahashi, A, Hiroi, N, Shibata, Y, Iwanaga, N, Kitano, H & Amano, H 2005, A framework for ODE-based multimodel biochemical simulations on an FPGA. in Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL., 1515788, Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL, vol. 2005, pp. 574-577, 2005 International Conference on Field Programmable Logic and Applications, FPL, Tampere, Finland, 05/8/24. https://doi.org/10.1109/FPL.2005.1515788

Osana Y, Fukushima T, Yoshimi M, Iwaoka Y, Funahashi A, Hiroi N et al. A framework for ODE-based multimodel biochemical simulations on an FPGA. In Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. 2005. p. 574-577. 1515788. (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2005.1515788

Osana, Yasunori ; Fukushima, Tomonori ; Yoshimi, Masato ; Iwaoka, Yow ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Iwanaga, Naoki ; Kitano, Hiroaki ; Amano, Hideharu. / A framework for ODE-based multimodel biochemical simulations on an FPGA. Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. 2005. pp. 574-577 (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL).

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AU - Hiroi, Noriko

AU - Shibata, Yuichiro

AU - Iwanaga, Naoki

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A framework for ODE-based multimodel biochemical simulations on an FPGA

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出版物シリーズ

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ASJC Scopus subject areas

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