General scheme of the two-stage flux balance analysis (FBA) method for drug target identification. Given a metabolic pathway related to a disease (a), our two-stage FBA method first calculates optimal fluxes of reactions and mass flows of metabolites in the pathologic state (b). Then, assuming some medication strategy can adjust the abnormal level of the disease-causing compound (the node marked in yellow), the two-stage FBA method determines the fluxes of reactions and the mass flows of metabolites with minimum side effects in the medication state (b). Different colors of the edges in (b) represent different fluxes. By comparing the reaction fluxes in the pathologic state and medication state (c), a sub-network is constructed and potential drug targets (the node marked in red) are identified (d).