Basically, a metabolic network is an assembly of biochemical reactions. While information about reactions is sufficient for modeling the network, the more information on associated genes or proteins, the more useful for the investigation of cellular responses in gene or protein level. Gene-protein-reaction (GPR) associations can be described in two-layer relations: “gene and protein” and “protein and reaction”, which are usually saved in spreadsheet format, the required information and available models are summarized in http://sb.nhri.org.tw/GEMsME/en/Metabolic_Models. On the other hand, published genome-scale metabolic models are commonly exchanged in Systems Biology Markup Language (SBML) format, but the protein information is lost or can not be recovered to the two-layer relation. Therefore, GEMsME provides different schema for these two types of metabolic reconstructions. If you want to create a project with clear two-layer relations of GPR associations, please check the checkbox of Gene-protein-reaction associations are necessary to generate the three-index schema (gene, protein and reaction indices) for reconstruction. Otherwise, GEMsME will generate the two-index schema (gene and reaction indices) automatically.

Reconstruction

Click on Reconstruction in the menu bar to open Model databases and Reference databases.

ü Model importing and editing

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. Some existing metabolic models can be found and downloaded from http://sb.nhri.org.tw/GEMsME/en/Metabolic_Models

You can directly edit/update the content of the imported model by right clicking on a cell.

In table of Reaction Index:

In table of Gene Index: