Gepasi

The Gepasi application was developed to be a software system for the simulation of chemical and biochemical kinetics. In this section basic concepts of (bio/chemical) kinetic models are explained. You can skip this section if you are familiar with this type of modelling.
Kinetic modelling is about describing the evolution of a system in time. A particular case of kinetic modelling deals with finding a state in which the system stops evolving in time. Such states are called steady states.
Bio/chemical kinetics deals with the change of chemical concentrations with time. The mathematical description of the changes is done via differential equations. Each variable metabolite concentration is then a differential equation and is composed of positive (production) and negative (destruction) contributions. These equations are known as balance equations, mainly because the two terms balance out in a steady state.
The terms that compose each balance equation alone also describe how the rates of reaction depend on the metabolite concentrations. This means that the change of one concentration is in general dependent on all the other concentrations and that is why we need software like Gepasi to produce numerical solutions of these equations.