Incremental and unifying modelling formalism for biological interaction networks

• Published in: BMC bioinformatics Vol. 8; no. 1; p. 433
• Main Authors: Yartseva, Anastasia, Klaudel, Hanna, Devillers, Raymond, Képès, François
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 08-11-2007; BioMed Central; BMC
• Subjects: Algorithms; Analysis; Animals; Bacteriophage lambda - genetics; Bacteriophage lambda - metabolism; Cell Physiological Phenomena; Computer Simulation; Feedback, Physiological; Formalism (Philosophy); Gene Expression Regulation; Genes, Switch - physiology; Genetic research; Humans; Methods; Models, Biological; Nonlinear Dynamics; Protein Interaction Mapping - methods; Sensitivity and Specificity; Signal Transduction; Stochastic Processes; Systems Biology - methods; User-Computer Interface; France
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-8-433

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 lambda 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.