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Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch

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Transactions on Computational Systems Biology VII

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 4230))

Abstract

We propose to model the dynamics of gene regulatory networks as concurrent processes in the stochastic pi calculus. As a first case study, we show how to express the control of transcription initiation at the lambda switch, a prototypical example where cooperative enhancement is crucial. This requires concurrent programming techniques that are new to systems biology, and necessitates stochastic parameters that we derive from the literature. We test all components of our model by exhaustive stochastic simulations. A comparison with previous results reported in the literature, experimental and simulation based, confirms the appropriateness of our modeling approach.

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Author information

Authors and Affiliations

  1. Interdisciplinary Research Institute, Lille, France

    CĂ©line Kuttler

  2. INRIA Futurs, Lille, France

    Joachim Niehren

Authors
  1. CĂ©line Kuttler
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  2. Joachim Niehren
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Editor information

Editors and Affiliations

  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo, (TN), Italy

    Corrado Priami

  2. Department of Computer Science, ReykjavĂ­k University, Kringlan 1, IS-103, ReykjavĂ­k, Iceland

    Anna IngĂłlfsdĂłttir

  3. Courant Institute of Mathematical Sciences, 10012, New York, NY, USA

    Bud Mishra

  4. Informatics and Mathematical Modelling, Technical University of Denmark,  

    Hanne Riis Nielson

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© 2006 Springer-Verlag Berlin Heidelberg

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Kuttler, C., Niehren, J. (2006). Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch. In: Priami, C., IngĂłlfsdĂłttir, A., Mishra, B., Riis Nielson, H. (eds) Transactions on Computational Systems Biology VII. Lecture Notes in Computer Science(), vol 4230. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11905455_2

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  • DOI: https://doi.org/10.1007/11905455_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-48837-8

  • Online ISBN: 978-3-540-48839-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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