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Process Calculi, Systems Biology and Artificial Chemistry

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Abstract

Knowledge about life processes develops through the interplay of theoretical speculation and experimental investigation. Both speculation and experiments present several difficulties that call for the development of faithful and accessible abstract models of the phenomena investigated. Several theories and techniques born in computer science have been proposed for the development of models that rely on solid formal bases and allow virtual experiments to be carried out computationally in silico.

This chapter surveys the basics of process calculi and their applications to the modeling of biological phenomena at a system level. Process calculi were born within the theory of concurrency for describing and proving properties of distributed interacting systems. Their application to biological phenomena relies on an interpretation of systems as made of interacting components exhibiting a computational kind of behavior, “cells as computation.”

The first seminal proposals and the subsequent enhancements for best adapting computer science theories to the domain of biology (with particular reference to chemical, biochemical, and cellular phenomena) are surveyed.

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Acknowledgments

The authors are deeply indebted to Luca Cardelli who kindly gave them permission to reuse here parts of his work, as well as Davide Chiarugi and Roberto Marangoni for joint previous work on VICE. The authors thank Enrico Cataldo for helpful comments and suggestions. The first author wishes to thank all the people at the Microsoft Research—University of Trento Centre for Computational and Systems Biology.

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Authors and Affiliations

  1. Dipartimento di Informatica, Università di Pisa, Pisa, Italy

    Pierpaolo Degano

  2. Department of Computing Science and Mathematics, University of Stirling, Stirling, UK

    Andrea Bracciali

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  1. Pierpaolo Degano
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  2. Andrea Bracciali
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Editors and Affiliations

  1. LIACS, Leiden University, Leiden, The Netherlands

    Grzegorz Rozenberg

  2. Computer Science Department, University of Colorado, Boulder, USA

    Grzegorz Rozenberg

  3. LIACS, Leiden University, Leiden, The Netherlands

    Thomas Bäck

  4. LIACS, Leiden University, Leiden, The Netherlands

    Joost N. Kok

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Degano, P., Bracciali, A. (2012). Process Calculi, Systems Biology and Artificial Chemistry. In: Rozenberg, G., Bäck, T., Kok, J.N. (eds) Handbook of Natural Computing. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92910-9_55

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