Automating AutoAnnotate

AutoAnnotate provides several commands which allow basic features to be automated via scripts, the command line or REST.


To call commands via REST the CyREST App is required. CyREST is normally installed by default.

CyRest is updated often. There are two ways to install the latest version:

  1. App Manager

    Open the App Manager dialog from the main menu at Apps > App Manager. Then go to the Check For Updates tab. If there is a newer version available it will be listed.

  2. App Store

    CyRest can also be installed or updated from the App Store Website

Command Documentation

CyREST Documentation

On-line documentation for AutoAnnotate commands can be accessed from the main menu at Help > Automation > CyREST Command API. This will open a web browser with documentation for all the commands that are available through CyREST. Navigate to the autoannotate entry and expand it for detailed documentation on each command.



For more details on Cytoscape Automation see the Cytoscape Automation Manual Page. For more details on using CyRest see the CyREST Documentation

Command Line Documentation

Open the Automation Panel from the main menu at View > Show Automation Panel.

Type help autoannotate to list the available commands provided by AutoAnnotate. To get help on a particular command type, for example the redraw command, type help autoannotate redraw.



For more details on the Automation Panel see the Cytoscape User Docs