HSIM: an hybrid stochastic simulation system for systems biology

Patrick Amar 1, 2 Loïc Paulevé 2
2 AMIB - Algorithms and Models for Integrative Biology
CNRS - Centre National de la Recherche Scientifique : UMR8623, X - École polytechnique, Inria Saclay - Ile de France, UP11 - Université Paris-Sud - Paris 11, LRI - Laboratoire de Recherche en Informatique, LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
Abstract : This paper describes a method to obtain in a certain sense the best of two well known simulation approaches: Stochastic simulation of chemical reactions and Entity-centered (multi-agents) systems. The stochastic simulation algorithm and its enhanced versions are adapted to simulate the behaviour of well stirred mixture of reactants when spatial localisation is not relevant; Conversely, in entity-centered methods, the causes and consequences due to spatial localisation are well handled. In terms of computational efficiency, the SSA methods are limited by the number of reactions and not by the amount of reactants, whereas it is the opposite for the entity-centered method. We will show how we can benefit from each approach, and also propose a new optimised algorithm for approximate stochastic simulation.
Type de document :
Communication dans un congrès
The Third International Workshop on Static Analysis and Systems Biology (SASB 2012), Sep 2012, Deauville, France. Electronic Notes in Theoretical Computer Science, 313, pp.3 -- 21, 2012, 〈10.1016/j.entcs.2015.04.016〉
Liste complète des métadonnées

https://hal.inria.fr/hal-00758168
Contributeur : Patrick Amar <>
Soumis le : mercredi 28 novembre 2012 - 11:37:30
Dernière modification le : mercredi 25 avril 2018 - 10:45:38

Lien texte intégral

Identifiants

Collections

Citation

Patrick Amar, Loïc Paulevé. HSIM: an hybrid stochastic simulation system for systems biology. The Third International Workshop on Static Analysis and Systems Biology (SASB 2012), Sep 2012, Deauville, France. Electronic Notes in Theoretical Computer Science, 313, pp.3 -- 21, 2012, 〈10.1016/j.entcs.2015.04.016〉. 〈hal-00758168〉

Partager

Métriques

Consultations de la notice

452