Incremental and unifying modelling formalism for biological interaction networks.
BACKGROUND
An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems.


RESULTS
We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into other formalisms, thus enabling a thorough study of the dynamic properties of a biological system. As a first illustration, we propose a translation into the R. Thomas' multivalued logical formalism which provides a possible semantics; a methodology for constructing such models is presented on a classical benchmark: the lambda phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system.


CONCLUSIONS
This approach provides an additional level of description between the biological and mathematical ones. It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way.
Yartseva
Anastasia
A
IBISC - Université d'Evry Val d'Essonne, Tour Evry 2, 523 place des Terrasses de l'Agora, F-91000 Evry, France. iartseva@gmail.com
Klaudel
Hanna
H
Devillers
Raymond
R
Képès
François
F
D000465:Algorithms; D000818:Animals; D010582:Bacteriophage lambda / Q000235:genetics / Q000378:metabolism; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D025461:Feedback, Physiological; D005786:Gene Expression Regulation; D005812:Genes, Switch / Q000502:physiology; D006801:Humans; D008954:Models, Biological; D017711:Nonlinear Dynamics; D025941:Protein Interaction Mapping / Q000379:methods; D012680:Sensitivity and Specificity; D015398:Signal Transduction; D013269:Stochastic Processes; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface