Through the interface of the UP Finder, after loading a Systems Biology Markup Language (SBML) model in the Organism item, all metabolites included in this model will be shown in the Targeted product item. Users can simply specify one metabolite as the target for overproduction. By choosing UPA in the Method option and running the program, a list of reaction names presented with their associated genes, reaction formulas, Yield and Ratio values will be returned as the output. All computation is based on the COBRA toolbox and MATLAB, and all optimization uses FBA for the solutions (Orth et al., 2010, Schellenberger et al., 2011). Initializing the COBRA toolbox is necessary in MATLAB before loading SBML models. The default uptake and growth constraints of the reconstructed model are used for the analysis. Users can also adjust the uptake and growth conditions to simulate metabolisms with special requirements. In addition, the UP Finder integrates FBA optimization in the Method option, which allows the basic function for computing growth rates under different conditions (Fig. 2). The UP Finder is freely available from GitHub (https://github.com/MEpathway/UP-Finder.git).Fig. 2The interface of the UP Finder. The interface contains 5 major functional units, including the Organism, Condition/Growth, Targeted product, Method and Output. Condition is the exchange reactions of SBML models with their constraints, and Growth indicates the specific biomass objective function (e.g. autotrophic or heterotrophic growth for Synechocystis sp. PCC 6803). Method contains two computational methods: UPA (up-regulated pathway analysis) and FBA (flux balance analysis).Fig. 2