The Cytoscape Automation app article collection
Related Experiment Video
Updated: Feb 8, 2026

Using an Automated Hirschberg Test App to Evaluate Ocular Alignment
Published on: March 24, 2020
Barry Demchak1, David Otasek1, Alexander R Pico2
1Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
Abstract:
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.
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