Structural simplification of chemical ...
Type de document :
Compte-rendu et recension critique d'ouvrage
Titre :
Structural simplification of chemical reaction networks in partial steady states
Auteur(s) :
Madelaine, Guillaume [Auteur]
BioComputing
Lhoussaine, Cedric [Auteur]
Niehren, Joachim [Auteur]
Linking Dynamic Data [LINKS]
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
BioComputing
Lhoussaine, Cedric [Auteur]
Niehren, Joachim [Auteur]
Linking Dynamic Data [LINKS]
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Titre de la revue :
BioSystems
Special Issue of CMSB'2015
Special Issue of CMSB'2015
Pagination :
34--49
Éditeur :
Elsevier
Date de publication :
2016-11-16
ISSN :
0303-2647
Mot(s)-clé(s) en anglais :
deterministic semantics
equivalence
system biology
chemical reaction network
structural simplification
equivalence
system biology
chemical reaction network
structural simplification
Discipline(s) HAL :
Informatique [cs]/Bio-informatique [q-bio.QM]
Chimie/Chimie théorique et/ou physique
Chimie/Chimie théorique et/ou physique
Résumé en anglais : [en]
We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can ...
Lire la suite >We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate interme- diate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten’s simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rule repeatedly and applied it to reaction networks from systems biology.Keywords: bioinformatics;systemsbiology;reactionnetwork;contextualequivalence.Lire moins >
Lire la suite >We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate interme- diate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten’s simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rule repeatedly and applied it to reaction networks from systems biology.Keywords: bioinformatics;systemsbiology;reactionnetwork;contextualequivalence.Lire moins >
Langue :
Anglais
Vulgarisation :
Non
Commentaire :
This is a journal extension of a paper published at the CMSB'2015 conference
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