Installation

It is recommended that you uninstall the previous version of the plugin before updating to avoid conflicts.

The KAM Navigator plugin can be installed over the web as a Cytoscape theme.

To install the KAM Navigator plugin:

1. Start Cytoscape and select Plugins -> Manage Plugins from the main menu. The plugin manager window will be displayed.
2. Click Settings tab at the top of the window. This will show the window that will allow you to add a new Plugins site.
3. Click the Add button to add a new Plugins download site.
4. Add the plugins folder as a new bookmark and click the Ok button. The KAM Navigator plugin location will be added to the Cytoscape bookmarks. The URL for the plugins is: https://raw.github.com/OpenBEL/Cytoscape-Plugins/master/plugins.xml
5. Select the bookmark you just created and the available plugins will be shown.
6. Navigate through the Theme folder and select the desired version of KAM Navigator. Information about the plugins will be shown in the right-hand panel. Click the Install button and the plugins will be downloaded and installed into your copy of Cytoscape.
7. Click the Close button to remove the window and return to Cytoscape.
8. To verify that the plugins were installed correctly, select Plugins from the main menu. There should be a menu item called KAM Navigator available. If you see this menu item, your plugins were successfully installed.

The KAM Navigator plugin can also be installed by copying the needed jar files webservice-0.9.jar and navigator-0.9.jar into the Cytoscape plugins directory. IMPORTANT: Any version of the plugin installed through the Plugin Manager should be uninstalled before attempting this.