Figure 1.

Source code describing a part of a small example in BNGL. In BNGL, model elements are specified in blocks enclosed in tags [17]. In this example, the upper block (lines 20–24) specifies the molecules and molecule domains. Three molecules are incorporated: molecule A with one binding site named b1, molecule R with the binding site b1 and the two modification sites p1 and p2 and molecule B with binding site b1. The lower block (lines 32–48) contains the reaction rules with patterns on the left and right of the <-> -symbols and kinetic parameters at the end of each reaction rule. For a complete specification of BNGL see [17].