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Implementation of ReCSiP: A ReConfigurable Cell SImulation Platform

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Book cover Field Programmable Logic and Application (FPL 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2778))

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Abstract

A reconfigurable accelerator for cell simulators called "ReCSiP" is proposed. It consists of both reconfigurable hardware and software platform. For high performance simulation, numerical solution of kinetic formulas, which require a large amount of computation, are processed on the reconfigurable hardware. It also provides programming interface for developing cell simulators. In this paper, Michaelis-Menten solver is designed and implemented on ReCSiP. The result of preliminary evaluation shows that ReCSiP is 8 times faster than Intel PentiumIII 1.13GHz when simple metabolic simulations are executed.

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References

  1. Schaff, J., et al.: The virtual cell. In: Proceedings of Pacific Symposium on Biocomputing, vol. 4, pp. 228–239 (1999)

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  2. Tomita, M., et al.: E-cell: software environment for whole-cell simulation. Bioinformatics 15(1), 72–84 (1999)

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  3. Takahashi, K., et al.: Computational challenges in cell simulation: A software engineering approach. In: IEEE Intelligent Systems, October 2002, pp. 64–71 (2002)

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, Keio University, 3-14-1 Hiyoshi, #223-8522, Kouhoku-ku, Yokohama, Japan

    Yasunori Osana, Tomonori Fukushima & Hideharu Amano

Authors
  1. Yasunori Osana
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  2. Tomonori Fukushima
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  3. Hideharu Amano
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Editor information

Editors and Affiliations

  1. Department of Electrical and Electronic Engineering, Imperial College London, Exhibition Road, SW7 2BT, London, UK

    Peter Y. K. Cheung

  2. Department of Electrical & Electronic Engineering, Imperial College London, Exhibition Road, SW7 2BT, London, UK

    George A. Constantinides

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© 2003 Springer-Verlag Berlin Heidelberg

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Osana, Y., Fukushima, T., Amano, H. (2003). Implementation of ReCSiP: A ReConfigurable Cell SImulation Platform. In: Y. K. Cheung, P., Constantinides, G.A. (eds) Field Programmable Logic and Application. FPL 2003. Lecture Notes in Computer Science, vol 2778. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45234-8_74

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  • DOI: https://doi.org/10.1007/978-3-540-45234-8_74

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40822-2

  • Online ISBN: 978-3-540-45234-8

  • eBook Packages: Springer Book Archive

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