Cells in silico: a holistic approach

Authors:
D. Chiarugi;P. Degano;J. B. Van Klinken;R. Marangoni
Affiliations:
Dipartimento di Scienze Matematiche e Informatiche, Università di Siena;Dipartimento di Informatica, Università di Pisa;Dipartimento di Scienze Matematiche e Informatiche, Università di Siena;Dipartimento di Informatica, Università di Pisa and Istituto di Biofisica, CNR, Pisa
Venue:
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Year:
2008

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Abstract

This paper reports on our experience in modelling whole cells with process calculi. We followed a holistic approach, aiming at investigating the behaviour of biological objects at the system level, in particular of a hypothetical and a of real prokaryote. These cells, namely VICE and Escherichia coli, have been specified through the π-calculus, endowed with a stochastic semantics. We describe a couple of variants of the π-calculus and briefly survey three interpreters of it, with increasing efficiency.We show how the usage of tools based on process calculi greatly helped us in designing the virtual cell VICE, and in comparing it with other prposals. The main properties of the in silico experiments on VICE and on Escherichia coli are then discussed and shown in agreement with those of real prokaryoptes acting in vivo/vitro.