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Cytoscape Automation Overview

Visit automation.cytoscape.org for a curated set of automation examples.

What is Cytoscape Automation

Cytoscape is a desktop-based tool that focuses on user-initiated operations for 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.

Also see our repo directories for Script Writers and for App Developers.

Experimental

Binder (for R)

Binder (for Python)

CircleCI (for R)

How to use the Binder environments

  • Launch RStudio or JupyterLab server by clicking the above Binder badges.
  • Run the following command in the RStudio Terminal tab or JupyterLab Terminal. This command launches Cytoscape Desktop in the background. The Cytoscape window is never visible.
    xvfb-run bash ~/cytoscape-unix-3.7.2/cytoscape.sh
    
  • Open .Rmd or .ipynb file with RStudio or JupyterLab and run the code chunks or cells. Feel free to modify any of the scripts and run commands directly, but note that your changes will not be saved. Binder only provides a temporary space to try out R and Python automation with Cytoscape.

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Collection of scripts that include programmatic io and control of Cytoscape

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