Starting with November 7, 2015 the source code of ModeRator - the Model Comparator is on GitHub: https://github.com/MartinsMednis/moderator
ModeRator - The Model Comparator can give insight about similarity of two models where entities' external identifiers, like, KEGG ID and ChEBI ID are not included.
Metabolites are compared using their names that are available in the model file. Chemical formulas, if available, are used to strengthen or weaken automatic decision about equality of metabolites. Formulas with different charge can be tolerated.
Reactions are compared based on their metabolites and stoichiometry. Balanced and imbalanced reactions can be compared through tolerance of missing reactants.
Models in SBML and COBRA spreadsheet format are supported.
M. Mednis, A. Vigants, Automatic comparison of metabolites names: impact of criteria thresholds, Biosystems and Information technology, 2(1), 2013, pp 1-5, DOI: http://dx.doi.org/10.11592/bit.130501
M. Mednis, V. Brusbardis, V. Galvanauskas, Comparison of genome-scale reconstructions using ModeRator, Proceedings of 13th IEEE International Symposium on Computational Intelligence and Informatics, Budapest, 2012, pp 79-84
M. Mednis, M. K. Aurich, Application of string similarity ratio and edit distance in automatic metabolite reconciliation comparing reconstructions and models, Biosystems and Information technology, vol 1(1), 2012, pp 14-18, DOI: http://dx.doi.org/10.11592/bit.121102