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Process calculi for biological processes

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Abstract

Systems biology is a research area devoted to developing computational frameworks for modeling biological systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to systems biology, based on the so-called process calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly expressive features to better reflect the biological aspects of interest. We then compare the expressive power of the resulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies.

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Notes

  1. A state (at time t) is given by the actual population of each species.

  2. Note the different usage of \(+\): while it stands for a nondeterministic choice in process calculi (hence a single alternative process runs), it indicates that both its arguments are present in a chemical equation.

  3. A tutorial on the eXtensible Markup Language is in XML.

  4. Molecular chaperones are proteins that assist the assembly, or disassembly, of other macromolecules.

  5. Alleles are variants of the same gene that determine differences in phenotypes.

  6. In a community of food web, the trophic link measures the distance of a species from the primary source of food.

  7. Interspecific interactions occur among members of different species.

  8. The subscript CY means that the phosphorylated molecule RELA-P is in the domain of the CYtoplasm

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Acknowledgements

We are deeply indebted with Grzegorz Rozenberg for many precious suggestions and advices on the structure of this work, and for having urged us to write this survey. We thank Corrado Priami and Chiara Bodei for many careful comments and remarks, as well as the anonymous reviewers for their detailed and very useful criticisms and recommendations that greatly helped us to improve our paper.

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Authors and Affiliations

  1. Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro, 2, 53100, Siena, Italy

    Andrea Bernini

  2. Dipartimento di Scienze Economiche e Aziendali, Università di Sassari, Via Muroni 25, 07100, Sassari, Italy

    Linda Brodo

  3. Dipartimento di Informatica, Università di Pisa, Largo B. Pontecorvo, 3, 56127, Pisa, Italy

    Pierpaolo Degano

  4. Dipartimento di Ingegneria dell’Informazione e Scienze Matematiche, Università di Siena, Via Roma, 56, 53100, Siena, Italy

    Moreno Falaschi

  5. Facultad de Ingeniería, Pontificia Universidad Javeriana, Calle 18 No 118-250, Cali, 760031, Colombia

    Diana Hermith

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  1. Andrea Bernini
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  2. Linda Brodo
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  3. Pierpaolo Degano
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Correspondence to Pierpaolo Degano.

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Bernini, A., Brodo, L., Degano, P. et al. Process calculi for biological processes. Nat Comput 17, 345–373 (2018). https://doi.org/10.1007/s11047-018-9673-2

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