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The Attributed Pi-Calculus with Priorities

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Transactions on Computational Systems Biology XII

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 5945))

Abstract

We present the attributed π− calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The λ-calculus serves as a constraint language underlying the π− calculus. Interaction constraints subsume priorities, by which to express global aspects of populations. We present a non-deterministic and a stochastic semantics for the attributed π− calculus. We show how to encode the π− calculus with priorities and polyadic synchronization π− @ and thus dynamic compartments, as well as the stochastic π− calculus with concurrent objects spico.

We illustrate the usefulness of the attributed π− calculus for modeling biological systems at two particular examples: Euglena’s spatial movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda. Furthermore, population-based model is supported beside individual-based modeling. A stochastic simulation algorithm for the attributed π− calculus is derived from its stochastic semantics. We have implemented a simulator and present experimental results, that confirm the practical relevance of our approach.

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Author information

Authors and Affiliations

  1. Institute of Computer Science, Modeling and Simulation Group, University of Rostock, Germany

    Mathias John & Adelinde M. Uhrmacher

  2. University of Lille 1, France

    Cédric Lhoussaine

  3. Inria, Lille, France

    Joachim Niehren

  4. BioComputing group, Lifl & Iri, Italy

    Cédric Lhoussaine & Joachim Niehren

Authors
  1. Mathias John
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  2. Cédric Lhoussaine
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  3. Joachim Niehren
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  4. Adelinde M. Uhrmacher
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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. Groningen Bioinformatics, University of Groningen, Centre, Kerklaan 30, 9751 NN, Haren, The Netherlands

    Rainer Breitling

  3. School of Information Systems, Brunel University, Kingston Lane, UB8 3PH, Uxbridge, UK

    David Gilbert

  4. Computer Science Institute, Brandenburg University of Technology, Walther-Pauer-Str. 2, 03046, Cottbus, Germany

    Monika Heiner

  5. Institute of Computer Science, University of Rostock, Joachim-Jungius-Str.10, 18059, Rostock, Germany

    Adelinde M. Uhrmacher

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John, M., Lhoussaine, C., Niehren, J., Uhrmacher, A.M. (2010). The Attributed Pi-Calculus with Priorities. In: Priami, C., Breitling, R., Gilbert, D., Heiner, M., Uhrmacher, A.M. (eds) Transactions on Computational Systems Biology XII. Lecture Notes in Computer Science(), vol 5945. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-11712-1_2

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  • DOI: https://doi.org/10.1007/978-3-642-11712-1_2

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  • Online ISBN: 978-3-642-11712-1

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