Cytoscape integration
The score networks, complex sets and purification datasets in ProCope can be exported to Cytoscape (http://www.cytoscape.org/) graphs.
Normal mode
When normally running the ProCope GUI, you can export the data objects to Cytoscape-compatible XGMML format. Use the Export to Cytoscape context-menu entries of the respective data object list (networks, complex sets or purification data).
Cytoscape plugin mode
ProCope can be integrated as a plugin into Cytoscape. Simply copy procope-X.Y.jar
from the lib/
directory to the plugin/
directory of Cytoscape. You can start the ProCope GUI from the Plugins menu of Cytoscape. Exporting a data object (see above) will then directly produce a new graph on the Cytoscape desktop.
Note: The resulting graphs are not layouted yet. The yFiles Circular and Organic layouts have shown to produce good layouts for the protein networks.