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
DOIs
Publication statusPublished - 2005 Dec 1
Event2005 International Conference on Field Programmable Logic and Applications, FPL - Tampere, Finland
Duration: 2005 Aug 242005 Aug 26

Publication series

NameProceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
Volume2005

Other

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

ASJC Scopus subject areas

  • Engineering(all)

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  • Cite this

    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