Simulating bacterial transcription and translation in a stochastic pi-calculus

Celine Kuttler (1, 2, 3)

1 IRI - Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq]
2 LIFL - Laboratoire d'Informatique Fondamentale de Lille
3 BioComputing - Programming Languages for Biological Modeling and Simulation

Stochastic simulation of genetic networks based on models in the stochastic pi-calculus is a promising recent approach. This paper contributes an extensible model of the central mechanisms of gene ex- pression i.e. transcription and translation, at the prototypical instance of bacteria. We reach extensibility through object-oriented abstractions, that are expressible in a stochastic π-calculus with pattern guarded inputs. We illustrate our generic model by simulating the effect of translational bursting in bacterial gene expression.

Domaines: Modélisation et simulation

Celine Kuttler. Simulating bacterial transcription and translation in a stochastic pi-calculus. Transactions on Computational Systems Biology, 2006, VI (4220), pp.113-149. ⟨hal-00460081⟩