Wikipedia describes flux-balance analysis as follows:
Flux Balance Analysis (FBA) is a mathematical method for analyzing metabolism. It does not require knowledge of metabolite concentration or details of the enzyme kinetics of the system. The assumption is made that the system being studied is homeostatic and the technique then aims to answer the question: given some known available nutrients, which set of metabolic fluxes maximizes the growth rate of an organism whilst preserving the internal concentration of metabolites?
We use flux-balance analysis for a number of purposes, but let us focus on just two key uses:
You can use FBA technology to predict which genes are essential under specific growth media.
You can predict which substrates the organism will be able to support growth. Specifically, we should, if our model is accurate, be able to predict growth under the conditions represented by Boiolog plates
That is, we construct an initial model of the reaction network from annotations, and then we "run" this model to make predictions (using FBA). When the predictions fail to match the reality, we must track down the causes of the discrepancies, update the model, and try again. This process has been used to rapidly identify incorrect annotations, and iteratively improve the annotations/models to achieve a consistent set of predictions.