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 are present in the target organism and obey Boolean statements as described in the reference reconstruction.
You can right click on a model to Generate simulation tables, so that a mathematical model including a stoichiometric 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, including