Normalizing Chemical Reaction Networks by ...
Document type :
Communication dans un congrès avec actes
Title :
Normalizing Chemical Reaction Networks by Confluent Structural Simplification
Author(s) :
Madelaine, Guillaume [Auteur]
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]
Université de Lille
Niehren, Joachim [Auteur]
BioComputing
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]

Université de Lille
Niehren, Joachim [Auteur]

BioComputing
Conference title :
14th International Conference on Computational Methods in Systems Biology (CMSB 2016)
Conference organizers(s) :
Ezio Bartocci
Pietro Lio
Nicola Paoletti
Pietro Lio
Nicola Paoletti
City :
Cambridge
Country :
Royaume-Uni
Start date of the conference :
2016-09-21
Book title :
Computational Methods in Systems Biology14th International Conference, CMSB 2016, Cambridge, UK, September 21-23, 2016, Proceedings
Journal title :
Lecture Notes in Bioinformatics
Publisher :
Springer
English keyword(s) :
system biology
chemical reaction networks
structural simplification
deterministic ODE semantics
chemical reaction networks
structural simplification
deterministic ODE semantics
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
English abstract : [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 ...
Show more >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.Show less >
Show more >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.Show less >
Language :
Anglais
Peer reviewed article :
Oui
Audience :
Internationale
Popular science :
Non
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