Figure 1. Representation of a metabolic network as a bipartite graph.
All edge stoichiometry labels are equal to 1 on default, except for the edge from r4 to C: according to the label of r4, this reaction produces 2C from E and and therefore both feeds the r2, r3, r4 cycle and produces the extra C consumed by rT. In addition, the input and output of compounds H and J through r2 ensures mass conservation by the cycle. Reactions rS1, rS2 and rH are boundary reactions because they do not show any incoming edges. The model seeds are {S1, S2, H} and rT is the targeted reaction, because it allows biomass F production, by definition exported from the cellular compartment with re (i.e., dashed line). The corresponding associated targeted metabolic compounds are then both A and C.