Cytoscape is a desktop-based tool that focuses on user-initiated operations generating user-consumable results. Cytoscape Automation enables users to create workflows executed entirely within Cytoscape or by external tools (e.g., Jupyter, R, GenomeSpace, etc), and whose results are reproducible. This enables Cytoscape to scale to large collections of datasets and to larger more complex workflows than is practical via keyboard and mouse.

Cytoscape Automation exists in two skins – the Commands interface and the Functions interface. Both can accomplish similar results, but are focused on different usage styles. Commands reprise user-initiated interactions (e.g., open session, import data, export image), whereas the Functions interface enables programmers to manipulate and operate on networks as internal Cytoscape data. Both Commands and Functions are available via a REST interface.

To learn more about Cytoscape Automation, visit our FAQ.

For resources for both Script Writers and Cytoscape App Authors, visit our Wiki.