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F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018.

The Cytoscape Automation app article collection.

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Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
Gladstone Institutes, San Francisco, CA, 95158, USA.
The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
University of California, San Francisco, San Francisco, CA, 94143, USA.
Institute for Systems Biology, Seattle, WA, 98109, USA.
Inistitut Pasteur, Paris, 75015, France.
Amsterdam Medical Centre, Ansterdam, 1105 AZ, Netherlands.


Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape's CyREST feature has allowed researchers to write workflows that call basic Cytoscape functions, but provides no access to its high value app-based functions. With Cytoscape Automation, workflows can now call apps that have been upgraded to expose their functionality. This article collection is a resource to assist readers in quickly and economically leveraging such apps in reproducible workflows that scale independently to large data sets and production runs.


App; Automation; Cytoscape; Network Analysis; Network Biology; Network Visualization

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