Figure 1

Example for the creation of an abstract syntax graph of a small model. This figure displays a unified representation of kinetic equations from an example model that consists of the following reactions:$R_1:\text{F1,6BP}\rightleftharpoons \text{DHAP}+\text{GA3P},R_2:\text{DHAP}\rightleftharpoons \text{GA3P}$. Both reactions are part of the glycolysis. The contained molecules are fructose 1,6-bisphosphate (F1,6BP), dihydroxyacetone phosphate (DHAP), and glyceraldehyde 3-phosphate (GA3P). Using the program SBMLsqueezer[31] the following mass action kinetics have been created:${\nu }_{R_1}=k_{+1}·\left[\text{F1,6BP}\right]-k_{-1}·\left[\text{DHAP}\right]·\left[\text{GA3P}\right],{\nu }_{R_2}=k_{+2}·$ [ DHAP]−k₋₂·[ GA3P]. The nodes for [DHAP] and [GA3P] are only contained in the syntax graph once and connected to more than one multiplication node. This figure clearly indicates that the syntax graph is not a tree. As can be seen in this picture, the outdegree of syntax trees does not have to be binary.