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Journal Article

Cytoscape Automation: empowering workflow-based network analysis


Boucas,  J.
Bioinformatics, Core Facilities, Max Planck Institute for Biology of Ageing, Max Planck Society;

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Otasek, D., Morris, J., Boucas, J., Pico, A. R., & Demchak, B. (2019). Cytoscape Automation: empowering workflow-based network analysis. Genome Biology, 20(1), 185. doi:10.1186/s13059-019-1758-4.

Cite as: https://hdl.handle.net/21.11116/0000-000B-41F7-5
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.