Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA

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

doi:10.1109/FPL.2005.1515809

Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA

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

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

10 Citations (Scopus)

Abstract

A reconfigurable biochemical simulator by solving ordinary differential equations has received attention as a personal high speed environment for biochemical researchers. For efficient use of the reconfigurable hardware, static scheduling of high-throughput arithmetic pipeline structures is essential. This paper shows and compares some scheduling alternatives, and analyzes the tradeoffs between performance and hardware amount. Through the evaluation, it is shown that the sharing first scheduling reduces the hardware cost by 33.8% in average, with the up to 11.5% throughput degradation. Effects of sharing of rate law functions are also analyzed.

Original language	English
Title of host publication	Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
Pages	666-669
Number of pages	4
DOIs	https://doi.org/10.1109/FPL.2005.1515809
Publication status	Published - 2005 Dec 1
Event	2005 International Conference on Field Programmable Logic and Applications, FPL - Tampere, Finland Duration: 2005 Aug 24 → 2005 Aug 26

Publication series

Name	Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
Volume	2005

Other

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

ASJC Scopus subject areas

Engineering(all)

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10.1109/FPL.2005.1515809

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Iwanagra, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., & Oguri, K. (2005). Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. In Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL (pp. 666-669). [1515809] (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; Vol. 2005). https://doi.org/10.1109/FPL.2005.1515809

Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. / Iwanagra, Naoki; Shibata, Yuichiro; Yoshimi, Masato et al.

Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. 2005. p. 666-669 1515809 (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; Vol. 2005).

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

Iwanagra, N, Shibata, Y, Yoshimi, M, Osana, Y, Iwaoka, Y, Fukushima, T, Amano, H , Funahashi, A, Hiroi, N, Kitano, H & Oguri, K 2005, Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. in Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL., 1515809, Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL, vol. 2005, pp. 666-669, 2005 International Conference on Field Programmable Logic and Applications, FPL, Tampere, Finland, 05/8/24. https://doi.org/10.1109/FPL.2005.1515809

Iwanagra N, Shibata Y, Yoshimi M, Osana Y, Iwaoka Y, Fukushima T et al. Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. In Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. 2005. p. 666-669. 1515809. (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL). doi: 10.1109/FPL.2005.1515809

Iwanagra, Naoki ; Shibata, Yuichiro ; Yoshimi, Masato et al. / Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. 2005. pp. 666-669 (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL).

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Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA

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