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context-specific-models

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Builds tissue-, cell-type-, and condition-specific metabolic models by integrating transcriptomic or proteomic data into a generic genome-scale model, using extraction algorithms (GIMME, iMAT, INIT/tINIT, MADE, E-Flux, CORDA, FASTCORE) via troppo and corda in Python or the COBRA Toolbox/RAVEN in MATLAB. Use when pruning a generic model to a context, choosing an extraction method and expression threshold, mapping expression through GPR rules to reactions, deciding whether an objective is required (GIMME vs iMAT), avoiding the growth-objective trap for non-proliferating tissue, or judging how much of a context-specific model is real signal versus an artifact of the threshold and method.

When to use

• pruning a generic model to a context
• choosing an extraction method and expression threshold
• mapping expression through GPR rules to reactions
• deciding whether an objective is required
• avoiding the growth-objective trap for non-proliferating tissue
• judging how much of a context-specific model is real signal versus an artifact

When not to use

• using cobra.flux_analysis.gimme() which does not exist

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