Comparative study of some methods for simulation of biochemical reactions

Patrick Amar 1, 2
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : In this course we will present some of the simulation methods most widely used to study the dynamics of biological networks. These networks may be metabolic networks, gene regulatory networks, and also the interactions between these two types of networks. We will discuss three types of approaches : the deterministic continuous simulations (ordinary dierential equation systems) discrete stochastic simulations (Gillespie method) and "entity-centered" systems (HSIM). We will see in which cases these approaches are applicable and the assumptions they imply. These simulation methods will be illustrated through two examples : the study of a model of circadian clock in the cyanobacterium and the study of oscillating systems using activators / inhibitors.
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Submitted on : Tuesday, December 11, 2012 - 10:26:18 AM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM

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Patrick Amar. Comparative study of some methods for simulation of biochemical reactions. Ecole de Printemps 2012 de la Société Francophone de Biologie Théorique, Jun 2012, Saint Flour, France. ⟨hal-00763571⟩

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