Schematic of sampling and scoring analysis to determine intracellular flux changes. (A) Reaction fluxes are sampled for two conditions. (B & C) Sample of flux differences is calculated by selecting random flux values from each condition to obtain a distribution of flux differences for each reaction. (D) Standardized reaction Z-scores are determined, which represent how far the sampled flux differences deviates from a zero flux change. Reaction scores can be used in visualizing perturbation subnetworks and analyzing reporter metabolites and subsystems.