In section the theoretical basics used in the simulation are sketched, how the simulator works. This part uses many references to the real theoretical works and sometimes borrows text and figures from them.

The simulator is working at the signalling and communication level, so do not expect something like calculating gradients or concentrations. However, the computational routines are formed in such a way that the simple approach taken in the simulator, can be easily replaced by solving the corresponding differential equations, and the other computational routines will not notice the change.

We discuss the basic terms to the absolutely necessary depth only