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Process Calculi Abstractions for Biology

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Algorithmic Bioprocesses

Part of the book series: Natural Computing Series ((NCS))

Abstract

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri nets theory and others by stochastic processes.

A most recent approach consists in interpreting living entities as terms of process calculi, by composition of a few behavioural abstractions. This paper comparatively surveys the state of the art of the process calculi approach to biological modelling.

The modelling features of a set of calculi are tested against a simple biological scenario, and available extensions and tools are briefly commented upon.

This work has been partially sponsored by the PRIN 2006 Project BISCA—Sistemi e calcoli di ispirazione biologica e loro applicazioni and by the FIRB project RBPR0523C3.

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Author information

Authors and Affiliations

  1. Laboratory for Foundations of Computer Science, The University of Edinburgh, Informatics Forum, 10 Crichton Street, EH8 9AB, Edinburgh, UK

    Maria Luisa Guerriero

  2. Dipartimento di Medicina Sperimentale e Clinica, Università “Magna Graecia” di Catanzaro, Catanzaro, Italy

    Davide Prandi

  3. Dipartimento di Ingegneria e Scienza dell’Informazione, Università di Trento, Trento, Italy

    Corrado Priami & Paola Quaglia

  4. The Microsoft Research, University of Trento Centre for Computational and Systems Biology, Trento, Italy

    Corrado Priami

Authors
  1. Maria Luisa Guerriero
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  2. Davide Prandi
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  3. Corrado Priami
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  4. Paola Quaglia
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Corresponding author

Correspondence to Maria Luisa Guerriero .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of British Columbia, Main Mall 201-2366, Vancouver, V6T 1Z4, Canada

    Anne Condon

  2. Dept. Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    David Harel

  3. Leiden Inst. Advanced Computer Science, Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, Netherlands

    Joost N. Kok

  4. Turku Centre for Computer Science, Lemminkaisenkatu 14 A, Turku, 20520, Finland

    Arto Salomaa

  5. Computer Science, Computation,, California Inst. of Technology, Pasadena, 91125, U.S.A.

    Erik Winfree

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Guerriero, M.L., Prandi, D., Priami, C., Quaglia, P. (2009). Process Calculi Abstractions for Biology. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_23

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