In this version of the UP Finder, not all metabolites listed in the reconstructed model will have valid results. It is usually good for analyzing terminal metabolites, such as secondary metabolites. For metabolites with considerable degradation pathways, it may not have valid results because the up-regulated flux would be further consumed by the degradation without accumulation. Since the evaluation process only works for single pathway, the UP Finder does not provide the best combination of overexpression yet in this version. To achieve accurate prediction and high identity with experimental verification, a high quality of metabolic network reconstruction is necessary. Some current SBML models such as E. coli (iJO1366.xml), and Synechocystis sp. PCC 6803 (iJN678.xml) have been tested with valid outputs in this UP Finder. Analysis examples demonstrated that the UP Finder is feasible to analyze gene overexpression targets for overproducing secondary metabolites and complex metabolic pathways, such as fatty acid biosynthesis. Given the decreasing cost of DNA synthesis, fast strain development for overproducing targeted products is becoming possible based on the large-scale DNA synthesis. Therefore, a user-friendly interfacial modeling tool that provides rapid pathway design would play an important role in the era of synthetic biology (Gibson, 2014, Kosuri and Church, 2014, Wang et al., 2011).