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: ClassDefinitions.py, the code for defining all the formats used by MetaMerge internally; FeatureMatching.py, the code for matching species, reactions based on the available features; FeaturePreparation.py, the code for extracting metabolite and reaction features from text; GeneProcessing.py, the code for processing gene information; MatchProcessing.py, the code for processing the metabolite and reaction matching matrices; MetaboliteMatching.py, the code for generating and processing closely matching metabolites; MetaMerge.py, an initializer for the other modules required by the MetaMerge algorithm; MetaMergeCore.py, the user interface of MetaMerge for preparing the matching matrices; ModelParsing.py, the user interface for parsing a metabolic model in Excel or SBML format; NetworkMerging.py, the code for merging two networks based on their matching matrices; OutputProcessing.py, the code for processing the output of the MetaMerge algorithm; ReactionMatching.py, the code for generating and processing closely matching reactions; Unrelated.py, the code for analyzing a metabolic network, not directly related to MetaMerge; Utilities.py, 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  and 2 , 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