Incremental and unifying modelling formalism for biological interaction networks

• Main Authors: Képès François, Devillers Raymond, Klaudel Hanna, Yartseva Anastasia
• Format: Article
• Language: English
• Published: BMC 2007-11-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/8/433

<p>Abstract</p> <p>Background</p> <p>An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems.</p> <p>Results</p> <p>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 <it>λ </it>phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system.</p> <p>Conclusion</p> <p>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.</p>