Flow chart for the MetaMerge algorithm. Shown is a flow chart of the six stages of the MetaMerge algorithm. Stage 1: the two models to be merged are parsed and the features for metabolites and reactions are prepared. Stage 2: an initial matching of reactions and metabolites is created. Stage 3: the user is asked to confirm the newly matched reactions and metabolites (optional step). Stage 4: the newly matched metabolites are used to extend the current matching of reactions and metabolites. Stages 3 and 4 are repeated until convergence. Stage 5: the matching of metabolites is checked to ensure transitivity and non-transformability. Stage 6: the merger is performed and the resulting network is output in the desired format. Circles indicate metabolites (red, model 1; white, model 2; pink, combined); squares indicate reactions (turquoise, model 1; brown, model 2; dark green, combined). The mini-networks were created using the Cytoscape software , version 2.7.0.