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An Implementation for Mapping SBML to BioSPI

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Fuzzy Systems and Knowledge Discovery (FSKD 2005)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3614))

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Abstract

The Systems Biology Markup Language(SBML) is an XML-based format for representing models of Systems Biology. BioSPI is a formal model to simulate biological systems, which is evolved from process calculi. Based on the previous research on modeling Systems Biology using process algebra, we propose a method to map SBML to BioSPI. The motivation of the work is to make full use of BioSPI to analyze biological systems described by SBML. In this paper, the mapping rules are presented and an example is given to show the simulation results.

The work is supported by The National Distinguished Young Scientist Fund of NNSFC (60225012), BDCC (03DZ14025), The National Nature Science Foundation of China (60473006), MSRA, and The BoShiDian Research Fund (20010248033).

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References

  1. Hucka, M., Finney, A., Sauro, H., et al.: Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions., Available via the World Wide Web at http://www.sbml.org

  2. Heiner, M., Koch, I., Voss, K.: Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets. In: 3rd Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, pp. 15–34 (2001)

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Author information

Authors and Affiliations

  1. BASICS, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China

    Zhupeng Dong, Xiaoju Dong, Xian Xu & Yuxi Fu

  2. BDCC, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China

    Zhizhou Zhang & Lin He

Authors
  1. Zhupeng Dong
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  2. Xiaoju Dong
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  3. Xian Xu
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  4. Yuxi Fu
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  5. Zhizhou Zhang
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  6. Lin He
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Editor information

Editors and Affiliations

  1. School of Electrical and Electronic Engineering, Nanyang Technological University, Block S1, Nanyang Avenue, 639798, Singapore

    Lipo Wang

  2. Honda Research Institute Europe GmbH, Offenbach/Main, Germany

    Yaochu Jin

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© 2005 Springer-Verlag Berlin Heidelberg

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Dong, Z., Dong, X., Xu, X., Fu, Y., Zhang, Z., He, L. (2005). An Implementation for Mapping SBML to BioSPI. In: Wang, L., Jin, Y. (eds) Fuzzy Systems and Knowledge Discovery. FSKD 2005. Lecture Notes in Computer Science(), vol 3614. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11540007_145

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  • DOI: https://doi.org/10.1007/11540007_145

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28331-7

  • Online ISBN: 978-3-540-31828-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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