Download Cytoscape User Manual

Cytoscape User Manual
down to find the plugin, click on the appropriate link to download the file, and then save it in the Cytoscape/plugins folder on your hard drive.
• Cytoscape will require a restart in order to load the manually installed plugin.
• If the plugin does not appear in the Currently Installed folder of the Plugin Manager, then Cytoscape
was unable to load the plugin. Your command line will display the error message generated.
Delete Existing Plugins
To delete an existing plugin or theme, go to the Plugin Manager at Plugins → Manage Plugins, click on
the appropriate plugin once to select it, and then click the Delete button at the bottom of the manager. It
is best to avoid deleting core plugins, as this may cause Cytoscape or other plugins to malfunction. A plugin
will be completely deleted after you have restarted Cytoscape.
Update Existing Plugins
Going to Plugins → Update Plugins will result in Cytoscape automatically accessing the Internet to look
for updated versions of the plugins you have installed. If newer versions are available, Cytoscape will then
display the available updates in the Plugin Manager; otherwise, it will inform you that there are no updatable
plugins. When multiple updates are detected, you will have the option to download some or all of the updates.
Some updates may require re-accepting the license before the download will begin. All updates require
Cytoscape to be restarted in order for the update to be fully installed. After clicking the Update All or
Update Selected buttons, a progress bar will appear showing the status of the download; it will disappear
once the update is complete, and the Plugin Manager can then be closed by clicking the Close button.
Note: The Update All button will update all listed plugins to the newest available version. If you prefer a
different version, select the name and click Update Selected.
Download Plugins from a Custom Site
The Plugin Manager automatically connects to the Cytoscape website and the sites of registered Cytoscape
plugins to check for and download any available plugins and updates. To change this setting, open the
Plugin Manager (by going to Plugins → Manage Plugins) and click the Change Download Site button.
You will be asked to choose a site from a preset list of bookmarks. Select one and click Ok. Alternatively,
click the Add Site button to open the Bookmark Manager and modify the list of bookmarks. In the Bookmark
Manager, choose the plugins category from the dropdown list, and then add/edit/delete URLs using the
appropriate buttons on the right-hand side of the window. After the correct site is selected, set it as the
download site by clicking OK. The Plugin Manager will refresh using that site.
Note: Custom download sites added from the Plugin Manager are not currently saved when you exit
Cytoscape.
CytoPanels
What are CytoPanels?
CytoPanels are floatable/dockable panels designed to cut down on the number of pop-up windows within
Cytoscape and to create a more unified user experience. These panels used to be called CytoPanel 1, 2,
and 3. From 2.5, they are named based on their functions. The following screenshot shows the file
yeastHighQuality.sif and GO annotations loaded into Cytoscape, performed Force-Directed layout, enable
Align and Distribute tools, and then run MCODE plugin for the data sets. In Control Panel (at the left-
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