Normalizing Chemical Reaction Networks by ...
Type de document :
Communication dans un congrès avec actes
Titre :
Normalizing Chemical Reaction Networks by Confluent Structural Simplification
Auteur(s) :
Madelaine, Guillaume [Auteur]
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]
Niehren, Joachim [Auteur]
BioComputing
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]
Niehren, Joachim [Auteur]
BioComputing
Titre de la manifestation scientifique :
14th International Conference on Computational Methods in Systems Biology (CMSB 2016)
Organisateur(s) de la manifestation scientifique :
Ezio Bartocci
Pietro Lio
Nicola Paoletti
Pietro Lio
Nicola Paoletti
Ville :
Cambridge
Pays :
Royaume-Uni
Date de début de la manifestation scientifique :
2016-09-21
Titre de l’ouvrage :
Computational Methods in Systems Biology14th International Conference, CMSB 2016, Cambridge, UK, September 21-23, 2016, Proceedings
Titre de la revue :
Lecture Notes in Bioinformatics
Éditeur :
Springer
Mot(s)-clé(s) en anglais :
system biology
chemical reaction networks
structural simplification
deterministic ODE semantics
chemical reaction networks
structural simplification
deterministic ODE semantics
Discipline(s) HAL :
Informatique [cs]/Bio-informatique [q-bio.QM]
Résumé en anglais : [en]
Reaction networks can be simplified by eliminating linear intermediate species in partial steady states. In this paper, we study the question whether this rewrite procedure is confluent, so that for any given reaction ...
Lire la suite >Reaction networks can be simplified by eliminating linear intermediate species in partial steady states. In this paper, we study the question whether this rewrite procedure is confluent, so that for any given reaction network, a unique normal form will be obtained independently of the elimination order. We first contribute a counter example which shows that different normal forms of the same network may indeed have different structures. The problem is that different “dependent reactions” may be introduced in different elimination orders. We then propose a rewrite rule that eliminates such dependent reactions and prove that the extended rewrite system is confluent up to kinetic rates, i.e., all normal forms of the same network will have the same structure. However, their kinetic rates may still not be unique, even modulo the usual axioms of arithmetics. This might seem surprising given that the ODEs of these normal forms are equal modulo these axioms.Lire moins >
Lire la suite >Reaction networks can be simplified by eliminating linear intermediate species in partial steady states. In this paper, we study the question whether this rewrite procedure is confluent, so that for any given reaction network, a unique normal form will be obtained independently of the elimination order. We first contribute a counter example which shows that different normal forms of the same network may indeed have different structures. The problem is that different “dependent reactions” may be introduced in different elimination orders. We then propose a rewrite rule that eliminates such dependent reactions and prove that the extended rewrite system is confluent up to kinetic rates, i.e., all normal forms of the same network will have the same structure. However, their kinetic rates may still not be unique, even modulo the usual axioms of arithmetics. This might seem surprising given that the ODEs of these normal forms are equal modulo these axioms.Lire moins >
Langue :
Anglais
Comité de lecture :
Oui
Audience :
Internationale
Vulgarisation :
Non
Collections :
Source :
Fichiers
- https://hal.archives-ouvertes.fr/hal-01348303/document
- Accès libre
- Accéder au document
- https://hal.archives-ouvertes.fr/hal-01348303/document
- Accès libre
- Accéder au document
- https://hal.archives-ouvertes.fr/hal-01348303/document
- Accès libre
- Accéder au document
- document
- Accès libre
- Accéder au document
- 1-hal-version.pdf
- Accès libre
- Accéder au document