Simplification of Reaction Networks, ...
Document type :
Compte-rendu et recension critique d'ouvrage
Title :
Simplification of Reaction Networks, Confluence and Elementary Modes
Author(s) :
Madelaine, Guillaume [Auteur]
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]
BioComputing
Niehren, Joachim [Auteur]
Linking Dynamic Data [LINKS]
BioComputing
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]

BioComputing
Niehren, Joachim [Auteur]

Linking Dynamic Data [LINKS]
BioComputing
Journal title :
Computation
Multiscale and Hybrid Modeling of the Living Systems
Multiscale and Hybrid Modeling of the Living Systems
Publisher :
MDPI
Publication date :
2017-02-28
ISSN :
2079-3197
English keyword(s) :
Deterministic semantics
Ordinary differential equations
Rewrite systems
System biology
Structural simplification
Elementary modes
Chemical reaction networks
Confluence
Ordinary differential equations
Rewrite systems
System biology
Structural simplification
Elementary modes
Chemical reaction networks
Confluence
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
Chimie/Chimie théorique et/ou physique
Chimie/Chimie théorique et/ou physique
English abstract : [en]
Reaction networks can be simplified by eliminating linear intermediate species in partialsteady states. In this paper, we study the question whether this rewrite procedure is confluent, sothat for any given reaction network ...
Show more >Reaction networks can be simplified by eliminating linear intermediate species in partialsteady states. In this paper, we study the question whether this rewrite procedure is confluent, sothat for any given reaction network with kinetic constraints, a unique normal form will be obtainedindependently of the elimination order. We first show that confluence fails for the elimination ofintermediates even without kinetics, if “dependent reactions” introduced by the simplification arenot removed. This leads us to revising the simplification algorithm into a variant of the doubledescription method for computing elementary modes, so that it keeps track of kinetic information.Folklore results on elementary modes then imply the confluence of the revised simplificationalgorithm with respect to the network structure, i.e., the structure of fully simplified networks is unique. We show however that the kinetic rates assigned to the reactions may not be unique, andprovide a biological example where two different simplified networks can be obtained. Finally, wegive a criterion on the structure of the initial network that is sufficient to guarantee the confluenceof both the structure and the kinetic rates.Show less >
Show more >Reaction networks can be simplified by eliminating linear intermediate species in partialsteady states. In this paper, we study the question whether this rewrite procedure is confluent, sothat for any given reaction network with kinetic constraints, a unique normal form will be obtainedindependently of the elimination order. We first show that confluence fails for the elimination ofintermediates even without kinetics, if “dependent reactions” introduced by the simplification arenot removed. This leads us to revising the simplification algorithm into a variant of the doubledescription method for computing elementary modes, so that it keeps track of kinetic information.Folklore results on elementary modes then imply the confluence of the revised simplificationalgorithm with respect to the network structure, i.e., the structure of fully simplified networks is unique. We show however that the kinetic rates assigned to the reactions may not be unique, andprovide a biological example where two different simplified networks can be obtained. Finally, wegive a criterion on the structure of the initial network that is sufficient to guarantee the confluenceof both the structure and the kinetic rates.Show less >
Language :
Anglais
Popular science :
Non
Comment :
Extended version of a conference paper at CMSB'2016
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