The rapid advances of constraint-based models provide the possibilities for quantitative evaluation of cellular metabolism (Bordbar et al., 2015, Kauffman et al., 2003), allowing to develop the standard method for rational pathway design. According to the annotated genome information, the reconstructed constraint-based models could represent the current knowledge of full metabolic reactions and their associated genes for an organism. With those constraint-based models, algorithms such as flux balance analysis (FBA) were developed to perform the in silico analysis of metabolic fluxes (Orth et al., 2010). Relying on the principle of mathematical optimization and mass balance, metabolic fluxes can be simulated within determined constraints. Such efforts have advanced the development of modeling approaches such as OptKnock (Burgard et al., 2003) that facilitates the procedures for identifying gene targets and pathway design.