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flux-balance-analysis

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Performs flux balance analysis (FBA), flux variability analysis (FVA), parsimonious FBA (pFBA), loopless FBA, flux sampling, and production envelopes on genome-scale metabolic models with COBRApy, solving the biomass-maximization linear program under a defined medium. Use when predicting growth rate on a carbon source, computing flux ranges and alternative optima (FVA), setting exchange bounds and minimal media, distinguishing a real growth phenotype from an under-constrained model, sampling the flux solution space, or choosing between FBA, pFBA, loopless FBA, and sampling for a flux distribution.

When to use

• predicting growth rate on a carbon source
• computing flux ranges and alternative optima (FVA)
• setting exchange bounds and minimal media
• distinguishing a real growth phenotype from an under-constrained model
• sampling the flux solution space
• choosing between FBA, pFBA, loopless FBA, and sampling
• production envelopes
• loopless FBA

When not to use

• validating actual intracellular fluxes
• 13C metabolic flux analysis
• metabolomics/isotope-tracing

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