What is ODE

In this chapter basic mathematical methods for the deterministic kinetic modeling of biochemical systems are described. Mathematical analysis methods, the respective algorithms, and appropriate tools and resources, as well as established standards for data exchange, model representations and definitions are presented. The methods comprise time-course simulations, steady state search, parameter scanning, and metabolic control analysis among others. An application is demonstrated using a test case model that describes parts of the extrinsic apoptosis pathway and a small example network demonstrates an implementation of metabolic control analysis.