Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch

Céline Kuttler 1 Joachim Niehren 2, 3, *
* Corresponding author
2 MOSTRARE - Modeling Tree Structures, Machine Learning, and Information Extraction
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
3 BioComputing - Programming Languages for Biological Modeling and Simulation
LIFL - Laboratoire d'Informatique Fondamentale de Lille
Abstract : We propose to model the dynamics of gene regulatory networks as concurrent processes in the stochastic pi calculus. As a first case study, we show how to express the control of transcription initiation at the lambda switch, a prototypical example where cooperative enhancement is crucial. This requires concurrent programming techniques that are new to systems biology, and necessitates stochastic parameters that we derive from the literature. We test all components of our model by exhaustive stochastic simulations. A comparison with previous results reported in the literature, experimental and simulation based, confirms the appropriateness of our modeling approach.
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Submitted on : Sunday, August 13, 2006 - 9:58:37 PM
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Céline Kuttler, Joachim Niehren. Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch. Transactions on Computational Systems Biology, Springer, 2006, Lecture Notes in Bioinformatics 4230 , pp.24-55. ⟨inria-00089218v2⟩

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