Starting with November 7, 2015 the source code of ModeRator - the Model Comparator is on GitHub:

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:

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:



The recommended method for new users is to run ModeRator in a virtual machine. In order to do this you will first need to install VirtualBox. For Linux or Mac I recommend installing virtualbox from your standard repository (aka "App store"). Windows users can find it on the VirtualBox website. Install VirtualBox, then follow the instructions below.

  1. Download ModeRator OVA file from our webserver.
  2. Start VirtualBox on your computer. Select Import appliance from the File menu and choose the the xubuntu_with_ModeRator_preinstalled_v1.ova file. Wait several minutes whilst this configures.
  3. ModeRator will appear on the VirtualBox Manager window. Select it and run it.
  4. Wait whilst xUbuntu starts up. The default user will login automatically. Click ModeRator launch icon on the desktop.


I have tested ModeRator on Ubuntu 12.10, Debian 7 and Fedora 20. The most straightforward installation is on Ubuntu. On other Linux distributions you may have to additionally set search path for libSBML.

If you would like to help me with porting ModeRator to other operating systems, please contact me.

Installation & dependencies

ModeRator 2.5 installation manual (for xUbuntu).