KEGG map loading

Click on Visualization in the menu bar to Load KEGG maps by either Import KEGG map (.xml) or Retrieve KEGG map depending on whether you have KGEE maps in hand.

If not, you can click on Setting in the menu bar to KEGG pathway Configure and set the link to where the KEGG pathway maps can be retrieved, e.g. http://www.genome.jp/kegg-bin/download.

Then you can retrieve KEGG pathway by choosing from the KEGG Pathway List.

The KEGG pathway map of rn00010:

We set rectangular nodes to represent reactions and define node name and node caption for each reaction. We directly use the entry name and reaction in KEGG maps as the node name and node caption respectively. Therefore, you can decide to Show node name or Show node caption by right clicking on a map.

Content of KEGG pathway map (rn00010.xml):

Content of KEGG pathway map (ec00010.xml):

Show node name: Show node caption:

You can extend other pathway maps in the map you have in the main network view window. A pathway map is represented in a rounded rectangle. We can move the pathway that you would like to extend to an empty region and right click on it to Extend map.

Map of Citrate cycle (TCA cycle) is extended in the map:

You can hold right-click button on the map and drag a rectangular region for selecting groups of objects, then right click over the selected objects to delete them all.

You can move identical objects close to each other. Select the identical objects and then right click on them to Merge all.

You can also load SBML models compatible to CellDesigner (http://www.celldesigner.org/index.html) to GEMSiRV. The SBML models for KEGG can be found and downloaded in http://www.systems-biology.org/001/001.html. You can click on Visualization in the menu bar to Load CellDesigner maps.

A SBML file eco00010.xml provided in http://sb.nhri.org.tw/GEMSiRV/en/Metabolic_Maps can be downloaded for demonstration.