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Natural Computing

, Volume 17, Issue 2, pp 345–373 | Cite as

Process calculi for biological processes

  • Andrea Bernini
  • Linda Brodo
  • Pierpaolo Degano
  • Moreno Falaschi
  • Diana Hermith
Article

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.

Keywords

Algorithmic Systems Biology In-silico simulation Functional and dynamic modeling Quantitative biology 

Notes

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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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Andrea Bernini
    • 1
  • Linda Brodo
    • 2
  • Pierpaolo Degano
    • 3
  • Moreno Falaschi
    • 4
  • Diana Hermith
    • 5
  1. 1.Dipartimento di Biotecnologie, Chimica e FarmaciaUniversità di SienaSienaItaly
  2. 2.Dipartimento di Scienze Economiche e AziendaliUniversità di SassariSassariItaly
  3. 3.Dipartimento di InformaticaUniversità di PisaPisaItaly
  4. 4.Dipartimento di Ingegneria dell’Informazione e Scienze MatematicheUniversità di SienaSienaItaly
  5. 5.Facultad de IngenieríaPontificia Universidad JaverianaCaliColombia

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