On the other hand, the Ratio parameter can be used for identifying functional metabolic modules. In the analysis examples, it was found that pathways with similar level of Ratio values presented the adjacent locations with regard to metabolic functions. For example, in Example 1 (Fig. 3), identified key pathways can be divided into 3 metabolic modules by their Ratio levels, including the initial MEP pathway synthesis module (dxs), the isoprenoid unit synthesis module (dxr, ispD, ispE, ispF, ispG, ispH), and the FPP synthesis module (idi, ispA). In Example 2 (Fig. 4), pathways with similar chain length of fatty acid synthesis also showed the similar levels on their Ratio values. In metabolic engineering of secondary metabolites and complex metabolic pathways, the imbalance of metabolic flux is a critical limiting factor for reaching high product yields. To coordinate the metabolic imbalance, engineering of module-based metabolic optimization has been regarded as a promising strategy for optimizing product yields (Ajikumar et al., 2010, Xu et al., 2013, Yadav et al., 2012, Zhao et al., 2013). Therefore, by taking advantage of the Ratio parameter, outputs of the UP Finder could also provide a quantitative basis for identifying functional metabolic modules in developing module-based optimization strategies.