ModeRator
Comparing two models with thousands of reactions is a big problem if models do not come from the same lab or are created using different standards. ModeRator can help here.
ModeRator - The Model Comparator compares two stoichiometric biological models (SBML or COBRA spreadsheet format) to identify common metabolites and reactions, even when external identifiers such as KEGG ID or ChEBI ID are not available.
Metabolites are compared using names from the model file. Chemical formulas, where available, strengthen or weaken the automatic matching decision; differences in charge can be tolerated. Reactions are compared based on their metabolites and stoichiometry, with configurable tolerance for missing reactants.
Originally developed by Martins Mednis during his PhD studies (actively developed until 2014), ModeRator is available in two forms: Web and Desktop.
Web version - no installation required, runs in any browser: https://moderator.mdr.lv · source [https://gitlab.com/moderator-the-model-comparator]
GTK desktop version - the original application, updated to run on modern Ubuntu desktops with a simplified setup: https://gitlab.com/mrtmednis/ModeRator
Citation
Mednis, M., Vigants A., (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information technology, 2(1), pp. 1–5. View full text.
Mednis, M., Brusbardis, V., Galvanauskas, V. (2012) Comparison of genome-scale reconstructions using ModeRator. In Proceedings of IEEE 13th International Symposium on Computational Intelligence and Informatics, Budapest, Hungary, November 20–22, 2012. INSPEC Accession Number: 13446376, 79–84. https://doi.org/10.1109/CINTI.2012.6496737.
Mednis, M., Aurich, M.K., (2012) Application of string similarity ratio and edit distance in automatic metabolite reconciliation comparing reconstructions and models. Biosystems and Information technology, 1(1), pp. 14–18. View full text.