Lyn-binding debugging. Reduced view: Ligand notation shortened to L and Rec shortened to R. If the user programs the rule that binds Lyn to Rec incorrectly (see Table 2), the corresponding contact map in (a) is missing the rule context information. The correct binding leads instead to the visualization in (b); the presence of the blue bubble set alerted the researcher to the difference and allowed them to debug their RBM. The incorrect formulation would allow at run time for the creation of the infinitely binding chain shown in (c).
Smith et al. BMC Bioinformatics 2012 13(Suppl 8):S3 doi:10.1186/1471-2105-13-S8-S3