Cytoscape Automation is a new feature that extends CyREST to enable reproducible, scalable, and novel network biology workflows. It allows Python and R workflows to interact with Cytoscape via REST-based API calls, using standardized JSON interfaces and Swagger documentation. Over 270 Cytoscape core functions and 34 apps are exposed as REST-callable functions. Python and R harmonization libraries (py2cytoscape and RCy3) provide easy access to Cytoscape functionality, with over 500 and 800 monthly downloads respectively. These libraries enable researchers to create reliable, flexible, and performant workflows quickly. Cytoscape Automation also introduces new standards for exposing Cytoscape functionality via REST-based API calls, backed by Swagger documentation. It supports both Function and Command interfaces for app automation, with Functions enabling complex parameter passing and Command interfaces allowing execution of Cytoscape commands similar to Unix or Windows terminal commands. The system includes improved documentation infrastructure, consistent mechanisms for calling CyREST and receiving return values, and enhanced coverage of core Cytoscape functionality. Cytoscape Automation is compatible with existing CyREST versions, with older versions returning results in a variety of JSON formats, while newer versions use a standardized CIResponse structure. The system also supports external workflows, enabling integration with Python and R best-of-breed libraries to create novel and repeatable results. Cytoscape Automation has been widely adopted, with over 300,000 downloads since its release in 2017, and is used to test automation-enabled apps and Cytoscape itself. Future development aims to further improve interoperability and workflow economics by expanding Cytoscape Automation to support more applications and services.Cytoscape Automation is a new feature that extends CyREST to enable reproducible, scalable, and novel network biology workflows. It allows Python and R workflows to interact with Cytoscape via REST-based API calls, using standardized JSON interfaces and Swagger documentation. Over 270 Cytoscape core functions and 34 apps are exposed as REST-callable functions. Python and R harmonization libraries (py2cytoscape and RCy3) provide easy access to Cytoscape functionality, with over 500 and 800 monthly downloads respectively. These libraries enable researchers to create reliable, flexible, and performant workflows quickly. Cytoscape Automation also introduces new standards for exposing Cytoscape functionality via REST-based API calls, backed by Swagger documentation. It supports both Function and Command interfaces for app automation, with Functions enabling complex parameter passing and Command interfaces allowing execution of Cytoscape commands similar to Unix or Windows terminal commands. The system includes improved documentation infrastructure, consistent mechanisms for calling CyREST and receiving return values, and enhanced coverage of core Cytoscape functionality. Cytoscape Automation is compatible with existing CyREST versions, with older versions returning results in a variety of JSON formats, while newer versions use a standardized CIResponse structure. The system also supports external workflows, enabling integration with Python and R best-of-breed libraries to create novel and repeatable results. Cytoscape Automation has been widely adopted, with over 300,000 downloads since its release in 2017, and is used to test automation-enabled apps and Cytoscape itself. Future development aims to further improve interoperability and workflow economics by expanding Cytoscape Automation to support more applications and services.