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• W2904241962 abstract "GEnome-scale Network REconstructions (GENREs) mathematically describe metabolic reactions of an organism or a specific cell type. GENREs can be used with a number of constraint-based reconstruction and analysis (COBRA) methods to make computational predictions on how a system changes in different environments. We created a simplified GENRE (referred to as iSIM) that captures central energy metabolism with nine metabolic reactions to illustrate the use of and promote the understanding of GENREs and constraint-based methods. We demonstrate the simulation of single and double gene deletions, flux variability analysis (FVA), and test a number of metabolic tasks with the GENRE. Code to perform these analyses is provided in Python, R, and MATLAB. Finally, with iSIM as a guide, we demonstrate how inaccuracies in GENREs can limit their use in the interrogation of energy metabolism." @default.
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• W2904241962 date "2019-02-01" @default.
• W2904241962 modified "2023-09-23" @default.
• W2904241962 title "A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools" @default.
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• W2904241962 doi "https://doi.org/10.1016/j.compbiomed.2018.12.010" @default.
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