The process for genome-scale model reconstruction. (1) Metabolic properties including associations between genes, enzymes and reactions were extracted from the genomic metabolic databases, stored and curated in an Excel spread-sheet; (2) a 2D reaction centric SBML representation was generated using an in house java application. (3) The stoichiometric matrix, as well as reversibility constraints and the objective function were extracted from the SBML; (4) the relevant linear programming problems were solved using the COBRA toolbox . (5) The model was refined in an iterative process, accessing the best available information in the literature and online data sources to achieve metabolic functionality.
Gomes de Oliveira Dal’Molin et al. BMC Genomics 2011 12(Suppl 4):S5 doi:10.1186/1471-2164-12-S4-S5