Software tool to model genetic regulatory networks Applications to segmental patterning in Drosophila

Based on the bimolecular mass action law and the derived mass conservation laws, we have proposed a mathematical framework in order to describe the regulation of gene expression in prokaryotes (F. Alves, R. Dilao, C. A,. Biologies 328 (2005)). Within this framework, a genetic regulatory network is described by a system of ordinary differential equations. As the number of equations increases exponentially with the number of genes and interactions in the network, we have developed a software package to write symbolically the associated system of differential equations. With this software package, GeNetSim, it is possible to follow in time the concentration of proteins and genes of the network. We show some applications of GeNetSim to the modeling of a genetic regulatory network involved in the segmentation of the embryo of Drosophila.