title: WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization.
abstract: 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. WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services. The WikiPathways app allows users to load pathways in two different views: as an annotated pathway ideal for data visualization and as a simple network to perform computational analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps. More than 3000 downloads in the first 12 months following its release in August 2013 highlight the importance and adoption of the app in the network biology field.
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, Netherlands.
authors.forename: Martina
authors.initials: M
authors.lastname: Kutmon
authors.affiliation: Gladstone Institutes, San Francisco, CA 94158-2261, USA.
authors.forename: Samad
authors.initials: S
authors.lastname: Lotia
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, Netherlands.
authors.forename: Chris T
authors.initials: CT
authors.lastname: Evelo
authors.affiliation: Gladstone Institutes, San Francisco, CA 94158-2261, USA.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico