Right click on Model databases to Import SBML file(.xml) or to Import spreadsheets(.xls), you can import a metabolic model in SBML/spreadsheet format as described in Metabolic Models.
You can directly edit/update the content of the imported model.
Right click on Reference databases to Import database(.xls), you can import a reference database provided in Reference Databases to create your own reference database.
You can add the information about metabolites and reactions described in a model to the reference database by right clicking on the metabolic model to add rxn&met to the Ref. DB.
A draft reconstruction can be generated by mapping a blank reconstruction outputed by GBKParser, containing gene information only, to a reference reconstruction. You just simply right click on the blank reconstruction to Draft a reconstruction
GEMsME will extract the reactions whose associated orthologous genes can be mapped to the reference reconstruction once the list of orthologous-gene pairs is available.
You can right click on a model to Generate simulation tables, so that a mathematical model including a stoichiometic matrix which describes the connectivity feature of the network and a default-defined systems boundaries can be generated.
With the generated simulation tables, you can identify dead-end metabolites.
Then, you can right click on the model with simulation tables to Define environmental conditions, e.g. the complete medium to simulate all extracellular metabolites can enter/exit the cell freely.
All analyses are implemented under the menu bar of Simulation.