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Cells in Silico: A Holistic Approach

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Formal Methods for Computational Systems Biology (SFM 2008)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 5016))

Abstract

This paper reports on our experience in modelling whole cells with process calculi. We followed a holistic approach, aiming at investigating the behaviour of biological objects at the system level, in particular of a hypothetical and a of real prokaryote. These cells, namely VICE and Escherichia coli, have been specified through the π-calculus, endowed with a stochastic semantics. We describe a couple of variants of the π-calculus and briefly survey three interpreters of it, with increasing efficiency. We show how the usage of tools based on process calculi greatly helped us in designing the virtual cell VICE, and in comparing it with other prposals. The main properties of the in silico experiments on VICE and on Escherichia coli are then discussed and shown in agreement with those of real prokaryoptes acting in vivo/vitro.

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Authors and Affiliations

  1. Dipartimento di Scienze Matematiche e Informatiche, Università di Siena,  

    Davide Chiarugi & Jan Bert Van Klinken

  2. Dipartimento di Informatica, Università di Pisa,  

    Pierpaolo Degano & Roberto Marangoni

  3. Istituto di Biofisica - CNR, Pisa

    Roberto Marangoni

Authors
  1. Davide Chiarugi
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  2. Pierpaolo Degano
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  3. Jan Bert Van Klinken
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  4. Roberto Marangoni
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Editor information

Marco Bernardo Pierpaolo Degano Gianluigi Zavattaro

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© 2008 Springer-Verlag Berlin Heidelberg

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Chiarugi, D., Degano, P., Van Klinken, J.B., Marangoni, R. (2008). Cells in Silico: A Holistic Approach. In: Bernardo, M., Degano, P., Zavattaro, G. (eds) Formal Methods for Computational Systems Biology. SFM 2008. Lecture Notes in Computer Science, vol 5016. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68894-5_10

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  • DOI: https://doi.org/10.1007/978-3-540-68894-5_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-68892-1

  • Online ISBN: 978-3-540-68894-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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