The MetNet XML Builder can build graph files for Cytoscape from pathways stored in MetNetDB. To create the files, simply check the "selected" boxes next to the pathways to be built, press the "Build" button, and select a destination folder. A separate file will be created for each selected pathway, as well as an "allSelectedPathways.xml" file that contains information about all the selected pathways.
By default, since RNA nodes are included in the graphs, gene nodes (which usually have no additional information) are left out. Checking the "Include Gene Nodes" box will include the gene nodes.
Some molecules, such as H2O, CO2, ATP, etc, participate in a lot of reactions. This can result in a graph file with a single node connected to several reactions. To remedy this, highly-connected entities can be duplicated for each reaction they participate in; in other words, rather than having a single node connected to ten reactions, ten identical nodes will be created and connected to a single reaction. Duplicated nodes usually look cleaner than highly-connected nodes.
The "Highly-connected Entities" tab lists a number of entities that can be cleaned. A check in the "Clean" box next to an entity indicates that the entity will be duplicated for every reaction it participates in. A list of commonly cleaned entities is selected by default.