title: A travel guide to Cytoscape plugins.
abstract: Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5-2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.
authors.affiliation: Department of Medicine, University of California, San Diego, La Jolla, California, USA.
authors.forename: Rintaro
authors.initials: R
authors.lastname: Saito
authors.forename: Michael E
authors.initials: ME
authors.lastname: Smoot
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Ono
authors.forename: Johannes
authors.initials: J
authors.lastname: Ruscheinski
authors.forename: Peng-Liang
authors.initials: PL
authors.lastname: Wang
authors.forename: Samad
authors.initials: S
authors.lastname: Lotia
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.forename: Trey
authors.initials: T
authors.lastname: Ideker
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D057225:Data Mining; D003628:Database Management Systems; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D005796:Genes / Q000502:physiology*; D023281:Genomics / Q000379:methods*; D008954:Models, Biological; D012984:Software