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Incremental and unifying modelling formalism for biological interaction networks

par Yartseva, Anastasia;Klaudel, Hanna;Devillers, Raymond ;Képès, François
Référence BMC bioinformatics, 8, 433
Publication Publié, 2007-11

Article révisé par les pairs

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Résumé :

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. © 2007 Yartseva et al; licensee BioMed Central Ltd.