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.

Keywords

WorkflowPython (programming language)JSONDocumentationComputer scienceAutomationBiologyWorld Wide WebData scienceSoftware engineeringBioinformaticsDatabaseProgramming languageEngineering

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Publication Info

Year
2019
Type
article
Volume
20
Issue
1
Pages
185-185
Citations
1656
Access
Closed

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David Otasek, John H. Morris, Jorge Bouças et al. (2019). Cytoscape Automation: empowering workflow-based network analysis. Genome biology , 20 (1) , 185-185. https://doi.org/10.1186/s13059-019-1758-4

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DOI
10.1186/s13059-019-1758-4