ODE Analysis of Biological Systems

This chapter aims to introduce some of the basics of modeling with ODEs in biology. We focus on computational, numerical techniques, rather than on symbolic ones. We restrict our attention to reaction-based models, where the biological interactions are mechanistically described in terms of reactions, reactants and products. We discuss how to build the ODE model associated to a reaction-based model; how to fit it to experimental data and estimate the quality of its fit; how to calculate its steady state(s), mass conservation relations, and its sensitivity coefficients. We apply some of these techniques to a model for the heat shock response in eukaryotes.