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.
Highlights
Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data
This article is included in the Cytoscape gateway
In 2014, the CyREST app[3] was created to allow external programs to exercise core Cytoscape functionality as part of custom workflows. By authoring such workflows in common languages, users can combine the best features of Cytoscape with those available in languagespecific libraries, creating new value much more quickly and cheaply than writing conventional Cytoscape apps
Summary
Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. This article is included in the Cytoscape gateway. Editorial Cytoscape is an open source software platform for interactive analysis, integration and visualization of networks and network data[1]. Cytoscape provides basic network analysis functionality (e.g., network import/export, network data analysis, visualization and layout) in a menu-driven desktop format.
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