Title :

Abstract Simulation of Reaction Networks via Boolean Networks

Author(s) :

Niehren, Joachim [Auteur]
Linking Dynamic Data [LINKS]
BioComputing
Vaginay, Athénaïs [Auteur]
Computational Algorithms for Protein Structures and Interactions [CAPSID]
Versari, Cristian [Auteur]
BioComputing
Université de Lille

English keyword(s) :

SBML
Logic
Boolean networks
Reaction networks
Sign abstraction
abstract interpretation
Linear equation systems
Systems biology

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]

English abstract : [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 ...
Show more >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 derivations 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 proof the soundness of our abstract simulation algorithm, discuss how we implemented it, illustrate it usefulness for exact reasoning, and show its applicability to reaction networks in SBML format from the BioModels database.Show less >

Language :

Anglais

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL

Submission date :

2022-05-18T02:08:23Z