The Journal of Biological Physics and Chemistry


Volume 4, Number 2, p. 64–73

The BioDyn language and simulator. Application to an immune response and E. coli and phage interaction

P. Ballet, A. Zemirline and L. Marcé

Département d¹Informatique, EA2215, Université de Bretagne Occidentale, BP 809, 29285 Brest CEDEX, France

In this paper we present a multiagent system coupled with a mass-spring system allowing biological processes to be simulated. This multiagent system uses dynamic graphs and their composition and decomposition operations. A graphical language is developed to facilitate the design of simulated biological mechanisms for non-computer scientists. The simulator and its associated language are called BioDyn (for Dynamical Biology). Finally, we show two examples of biological simulation to point out the abilities of our system.

Keywords: composition, computational biology, decomposition, dynamic graphs, mass-spring systems, multiagent systems

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