From ODES to Language-Based, Executable Models of Biological Systems

Modeling in biology is mainly grounded in mathematics, and specifically on ordinary differential equations (ODE). The programming language approach is a complementary and emergent tool to analyze the dynamics of biological networks. Here we focus on BlenX showing how it is possible to easily re-use ODE models within this framework. A budding yeast cell cycle example demonstrates the advantages of using a stochastic approach. Finally, some hints are provided on how the automatically translated model can take advantage of the full power of BlenX to analyze the control mechanisms of the cell cycle machinery.