Additional file 4.

The full code of the MetaMerge algorithm implemented in Python. The code is divided into 14 modules, each of which contains multiple functions, as follows:, the code for defining all the formats used by MetaMerge internally;, the code for matching species, reactions based on the available features;, the code for extracting metabolite and reaction features from text;, the code for processing gene information;, the code for processing the metabolite and reaction matching matrices;, the code for generating and processing closely matching metabolites;, an initializer for the other modules required by the MetaMerge algorithm;, the user interface of MetaMerge for preparing the matching matrices;, the user interface for parsing a metabolic model in Excel or SBML format;, the code for merging two networks based on their matching matrices;, the code for processing the output of the MetaMerge algorithm;, the code for generating and processing closely matching reactions;, the code for analyzing a metabolic network, not directly related to MetaMerge;, the code of miscellaneous auxiliary functions used by the MetaMerge algorithm. Additionally, the zipped directory contains a shelve file called Mappings with KEGG and Biocyc identifiers for the metabolites in both M. tuberculosis models extracted by Jeremy Zucker, and the cleaned-up and extended Excel files Mycobacterium tuberculosis 1.xls and Mycobacterium tuberculosis 2.xls for models 1 [13] and 2 [14], respectively, containing additional annotation contributed by Marina Druz.

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Chindelevitch et al. Genome Biology 2012 13:r6   doi:10.1186/gb-2012-13-1-r6