They are written by the app authors themselves according to a template that calls for explaining newly available functions, how they can be called, and with real world examples. This collection of Cytoscape app articles at F1000Research is intended to serve as a resource to researchers (as workflow authors) and app developers to understand the features and interfaces exposed by automation-enabled apps. As of March, 2018, app authors upgraded and released 22 apps. For an app to be callable, it must be upgraded to support automation via either a Commands or Functions interface. In 2018, Cytoscape Automation was created to enable external workflows to also call functionality in apps. Finally, external workflows enable reproducibility not available using Cytoscape’s standard mouse/keyboard/display interaction mode. Furthermore, such workflows can more easily integrate external applications (e.g., GenePattern and iGraph) and multiple large datasets. By authoring such workflows in common languages (such as R and Python), users can combine the best features of Cytoscape with those available in language-specific libraries, thus creating new value much more quickly and cheaply than writing conventional Cytoscape apps. In 2014, the CyREST app 3 was created to allow external programs to exercise core Cytoscape functionality as part of custom workflows. To date, Cytoscape users can choose among over 330 apps written by over 550 authors. Most importantly, it also enables and encourages users to add extensions (called apps) that deliver custom features important for specific workflows (e.g., ClueGO 2 for enrichment analysis relative to various ontologies). At heart, Cytoscape provides basic network analysis functionality (e.g., network import/export, network data analysis, visualization and layout) in a menu-driven desktop format. Cytoscape is an open source software platform for interactive analysis, integration and visualization of networks and network data 1.
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