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

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

3 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationProceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
Pages574-577
Number of pages4
Volume2005
DOIs
Publication statusPublished - 2005
Event2005 International Conference on Field Programmable Logic and Applications, FPL - Tampere, Finland
Duration: 2005 Aug 242005 Aug 26

Other

Other2005 International Conference on Field Programmable Logic and Applications, FPL
CountryFinland
CityTampere
Period05/8/2405/8/26

Fingerprint

Field programmable gate arrays (FPGA)
Simulators
Microprocessor chips
Chemical reactions
Throughput
Networks (circuits)
Communication

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., ... 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 (Vol. 2005, pp. 574-577). [1515788] 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. Vol. 2005 2005. p. 574-577 1515788.

Research output: Chapter in Book/Report/Conference proceedingConference 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. vol. 2005, 1515788, 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. Vol. 2005. 2005. p. 574-577. 1515788 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. Vol. 2005 2005. pp. 574-577
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