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Open Access Highly Accessed 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

Abstract

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

Conclusion

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.