Result: Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints

Title:
Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints
Authors:
DE MARIA, Elisabetta, FAGES, François, RIZK, Aurélien, SOLIMAN, Sylvain
Source:
Selected Papers from the 7th International Conference on Computational Methods in Systems BiologyTheoretical computer science. 412(21):2108-2127
Publisher Information:
Oxford: Elsevier, 2011.
Publication Year:
2011
Physical Description:
print, 46 ref
Original Material:
INIST-CNRS
Subject Terms:
Computer science, Informatique, Sciences exactes et technologie, Exact sciences and technology, Sciences et techniques communes, Sciences and techniques of general use, Mathematiques, Mathematics, Combinatoire. Structures ordonnées, Combinatorics. Ordered structures, Combinatoire, Combinatorics, Plans d'expériences et configurations, Designs and configurations, Analyse mathématique, Mathematical analysis, Calcul des variations et contrôle optimal, Calculus of variations and optimal control, Analyse numérique. Calcul scientifique, Numerical analysis. Scientific computation, Analyse numérique, Numerical analysis, Méthodes numériques en programmation mathématique, optimisation et calcul variationnel, Numerical methods in mathematical programming, optimization and calculus of variations, Optimisation et calcul variationnel numériques, Numerical methods in optimization and calculus of variations, Sciences appliquees, Applied sciences, Informatique; automatique theorique; systemes, Computer science; control theory; systems, Informatique théorique, Theoretical computing, Divers, Miscellaneous, Apprentissage, Learning, Aprendizaje, Biologie, Biology, Biología, Calcul automatique, Computing, Cálculo automático, Cinétique, Kinetics, Cinética, Contrainte, Constraint, Coacción, DNA, Formalisation, Formalization, Formalización, Informatique théorique, Computer theory, Informática teórica, Logique temporelle, Temporal logic, Lógica temporal, Méthode optimisation, Optimization method, Método optimización, Observation, Observación, Optimisation, Optimization, Optimización, Prédiction, Prediction, Predicción, Puissance, Power, Potencia, Réparation, Repair, Reparación, Résolution (math), Solving, Resolución (matemática), 03B44, 05Bxx, 49XX, 65K10, 65Kxx, 68T05, Cell cycle, Constraint solving, DNA damage, Irinotecan, Model checking, Model coupling, Parameter learning
Document Type:
Academic journal Article
File Description:
text
Language:
English
Author Affiliations:
EPI Contraintes, INRIA Paris-Rocquencourt, 78153 Le Chesnay, France
ISSN:
0304-3975
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=24108304
Rights:
Copyright 2015 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Computer science; theoretical automation; systems

Mathematics
Accession Number:
edscal.24108304
Database:
PASCAL Archive

Further Information

In systems biology, the number of available models of cellular processes has increased rapidly, but re-using models in different contexts or for different questions remains a challenging issue. In this paper, we study the coupling of different models playing a role in the mammalian cell cycle and in cancer therapies. We show how the formalization of experimental observations in temporal logic with numerical constraints can be used to compute the unknown coupling kinetics parameter values agreeing with experimental data. This constraint-based approach to computing with partial information is illustrated through the design of a complex model of the mammalian cell cycle, the circadian clock, the p53/Mdm2 DNA-damage repair system, the metabolism of irinotecan and the control of cell exposure to it. We discuss the use of this model for cancer chronotherapies and evaluate its predictive power with respect to circadian core gene knock-outs.