Abstract Simulation of Reaction Networks ...
Type de document :
Communication dans un congrès avec actes
Titre :
Abstract Simulation of Reaction Networks via Boolean Networks
Auteur(s) :
Niehren, Joachim [Auteur]
BioComputing
Linking Dynamic Data [LINKS]
Vaginay, Athénaïs [Auteur]
Computational Algorithms for Protein Structures and Interactions [CAPSID]
Versari, Cristian [Auteur]
BioComputing
BioComputing
Linking Dynamic Data [LINKS]
Vaginay, Athénaïs [Auteur]
Computational Algorithms for Protein Structures and Interactions [CAPSID]
Versari, Cristian [Auteur]
BioComputing
Titre de la manifestation scientifique :
CMSB 2022 - 20th International Conference on Computational Methods in Systems Biology
Ville :
Bucarest
Pays :
Roumanie
Date de début de la manifestation scientifique :
2022-09-14
Éditeur :
Springer
Mot(s)-clé(s) en anglais :
Systems biology
abstract interpretation
Sign abstraction
Reaction networks
Boolean networks
Logic
SBML
Constraint programming
abstract interpretation
Sign abstraction
Reaction networks
Boolean networks
Logic
SBML
Constraint programming
Discipline(s) HAL :
Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]
Informatique [cs]
Résumé en anglais : [en]
We propose to simulate chemical reaction networks with the deterministic semantics abstractly, without any precise knowledge on the initial concentrations. For this, the concentrations of species are abstracted to Booleans ...
Lire la suite >We propose to simulate chemical reaction networks with the deterministic semantics abstractly, without any precise knowledge on the initial concentrations. For this, the concentrations of species are abstracted to Booleans stating whether the species is present or absent, and the derivatives of the concentrations are abstracted to signs saying whether the concentration is increasing, decreasing, or unchanged. We use abstract interpretation over the structure of signs for mapping the ODEs of a reaction network to a Boolean network with nondeterministic updates. The abstract state transition graph of such Boolean networks can be computed by finite domain constraint programming over the finite structure of signs. Constraints on the abstraction of the initial concentrations can be added naturally, leading to an abstract simulation algorithm that produces only the part of the abstract state transition graph that is reachable from the abstraction of the initial state. We prove the soundness of our abstract simulation algorithm, discuss its implementation, and show its applicability to reaction networks in the SBML format from the BioModels database.Lire moins >
Lire la suite >We propose to simulate chemical reaction networks with the deterministic semantics abstractly, without any precise knowledge on the initial concentrations. For this, the concentrations of species are abstracted to Booleans stating whether the species is present or absent, and the derivatives of the concentrations are abstracted to signs saying whether the concentration is increasing, decreasing, or unchanged. We use abstract interpretation over the structure of signs for mapping the ODEs of a reaction network to a Boolean network with nondeterministic updates. The abstract state transition graph of such Boolean networks can be computed by finite domain constraint programming over the finite structure of signs. Constraints on the abstraction of the initial concentrations can be added naturally, leading to an abstract simulation algorithm that produces only the part of the abstract state transition graph that is reachable from the abstraction of the initial state. We prove the soundness of our abstract simulation algorithm, discuss its implementation, and show its applicability to reaction networks in the SBML format from the BioModels database.Lire moins >
Langue :
Anglais
Comité de lecture :
Oui
Audience :
Internationale
Vulgarisation :
Non
Collections :
Source :
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