Map replacement

In order to ease the creation of customized maps, GEMSiRV provide a function in map replacement. You can right click on a map to Replace caption of nodes to convert the map to a customized map.

For example, we replace a KEGG map (e.g. rn00010.xml) to a Model SEED-based map by providing two separate lists for metabolite and reaction mapping. The KEEG to Model SEED mapping lists can be found and downloaded in http://sb.nhri.org.tw/GEMSiRV/en/Manual.

Therefore, some nodes of metabolite and reaction can be replaced to form a Model SEED-based map.

Please remember to save a map before closing it.

You can open a map saved in cartomap format.

In order to create a useful map for visualization, an interactive function between model reconstruction and map visualization is implemented in GEMSiRV.

For demonstration, we import a Model SEED model Acinetobacter sp. ADP1 (Opt 62977.3.xml).

You can filter reactions by comparing with the metabolic model you select and you can get the reaction lists for reactions not existing or existing in the model.

We select and delete the left list of reactions for creating a model-specific map.

You can remove those nodes of metabolite without linking to reaction by right clicking on the map to Remove nodes (met) without edges.

You can also filter reactions in a metabolic model by comparing with a map. Right click on the model to Filter reaction by a map and choose a map you want to compare with. Then you can get a comparison report as well as a temporary map including those reactions not present in the map you chosen.

A comparison report showing what reactions are present in the model only, in the map only, and in the both.

A temporary map including those reactions in the model but not in the map

You can save the temporary map and add it into the map you are working with.

Add a map by clicking Add a map in the toolbar and dropping in an empty region of the map and extend the map by right clicking on the added map to Extend map.