WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

In this paper we present the open-source WikiPathways app for Cytoscape http://apps.cytoscape.org/apps/wikipathways) that can be used to import biological pathways for data visualization and network analysis. an open, collaborative biological pathway database that provides fully pathway diagrams for manual download or through web services. The app allows users to load pathways in two different views: as an ideal for data visualization and as a simple network to perform analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and together with other apps. More than 3000 downloads in the first 12 following its release in August 2013 highlight the importance and app in the network biology field.