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A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems

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Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living (IWANN 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5518))

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Abstract

Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling. We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating different biological networks. Aware that no formalism can fit all purposes we realize Petri nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework for regulatory and metabolic networks.

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Author information

Authors and Affiliations

  1. IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal

    Daniel Machado, Rafael S. Costa, Isabel Rocha & Eugénio C. Ferreira

  2. Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal

    Miguel Rocha

  3. Department of Biological Engineering/Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

    Bruce Tidor

Authors
  1. Daniel Machado
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  2. Rafael S. Costa
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  3. Miguel Rocha
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  4. Isabel Rocha
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  5. Bruce Tidor
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  6. Eugénio C. Ferreira
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Editor information

Editors and Affiliations

  1. Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan

    Sigeru Omatu

  2. Department of Informatics / CCTC, University of Minho, Braga, Portugal

    Miguel P. Rocha

  3. MAmI Research Lab, University of Castilla-La Mancha,, Ciudad Real, Spain

    José Bravo

  4. Department of Informatics, University of Vigo, Ourense, Spain

    Florentino Fernández

  5. Grupo de Investigación GICAP, Área de Lenguajes Higher Polytechnic School, Universidad de Burgos, Burgos, Spain

    Emilio Corchado

  6. Higher Polytechnic School, University of Burgos, Burgos, Spain

    Andrés Bustillo

  7. Department of Informatics, University of Salamanca, Salamanca, Spain

    Juan M. Corchado

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© 2009 Springer-Verlag Berlin Heidelberg

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Machado, D., Costa, R.S., Rocha, M., Rocha, I., Tidor, B., Ferreira, E.C. (2009). A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. In: Omatu, S., et al. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02481-8_161

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  • DOI: https://doi.org/10.1007/978-3-642-02481-8_161

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02480-1

  • Online ISBN: 978-3-642-02481-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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