Fig. 5

Trap detection with VerifyModel.R. A A representative rxncon model flagged by VerifyModel.R as having inconsistent attractors upon repeated addition and removal of the ligand. B This is confirmed by plots of the full paths the network traverses upon the addition and removal of the ligand (attractors are striped, substrate states colored purple). C Automatically generated comparison plots reveal that the substrate remains phosphorylated in the first “no-ligand”attractor, but not in the second. D This “trap” behaviour is corrected by addition of a dephosphorylation reaction to produce a network (D) with consistent no-ligand attractors as shown in (E) and (F)