Cytoscape Automation: empowering workflow-based network analysis
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Updated: Jan 20, 2026

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
Published on: September 25, 2021
David Otasek1, John H Morris2, Jorge Bouças3
1Department of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA.
Abstract:
Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.
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