Interactions define layers. Processes (white boxes) are coupled by graded (red lines) and all-or-non interactions (green lines). All processes that are coupled by graded interactions are merged into the same module, which is called layer (blue boxes). Therefore, layers are only connected by all-or-none interactions. A) A small example system that is discussed in detail. Occurring processes are ligand binding, binding site phosphorylation and effector binding. The reaction scheme is shown in Figure 5. B) A larger example system that is discussed in Additional file 4. There, the successive arrangements of layers can be seen.