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Figure 1 | BMC Systems Biology

Figure 1

From: Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

Figure 1

Method summary. (I) The gene assigned with KO for each studied organism was downloaded from the IMG database or KEGG. (II) The KO was mapped with the reaction data set. (III) A draft model was exported to MS-Excel format by our function saveDraftModel, the draft model was mapped to KEGG maps using our function DrawPathway. (IV) The draft was curated manually from literature and other gene annotations in IMG files such as TIGRFAMs and Pfam. After this, the model was simulated using RAVEN and MOSEK. (V) The community interaction design described how the organisms share growth medium components. (VII) Community interaction was converted to XML format. (VIII) Both optCom and FBA models were generated from XML files.

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