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Open Access Highly Accessed Open Badges Research article

Incremental and unifying modelling formalism for biological interaction networks

Anastasia Yartseva1*, Hanna Klaudel1, Raymond Devillers2 and François Képès3

Author Affiliations

1 IBISC – Université d'Évry Val d'Essonne, Tour Evry 2, 523 place des Terrasses de l'Agora, F-91000 Evry, France

2 Département' d'Informatique, Université Libre de Bruxelles, CP212, B-1050 Bruxelles, Belgium

3 Epigenomics Project, Genopole®, CNRS & Université d'Evry Val d'Essonne, France

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BMC Bioinformatics 2007, 8:433  doi:10.1186/1471-2105-8-433

Published: 8 November 2007



An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems.


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 λ phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system.


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.