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It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump\u2010start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. 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Bioinform<\/jats:italic>\n                    . 47:8.13.1\u20108.13.24. \u00a9 2014 by John Wiley &amp; Sons, Inc.\n                  <\/jats:p>","DOI":"10.1002\/0471250953.bi0813s47","type":"journal-article","created":{"date-parts":[[2014,9,8]],"date-time":"2014-09-08T23:07:49Z","timestamp":1410217669000},"source":"Crossref","is-referenced-by-count":825,"title":["Biological Network Exploration with Cytoscape 3"],"prefix":"10.1002","volume":"47","author":[{"given":"Gang","family":"Su","sequence":"first","affiliation":[{"name":"Molecular Behavioral Neuroscience Institute, University of Michigan  Ann Arbor Michigan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John H.","family":"Morris","sequence":"additional","affiliation":[{"name":"Resource for Biocomputing, Visualization, and Informatics, University of California San Francisco  San Francisco California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry","family":"Demchak","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego  La Jolla California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary D.","family":"Bader","sequence":"additional","affiliation":[{"name":"The Donnelly Centre, University of Toronto  Toronto Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2014,9,8]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0004345"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-2"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.242"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl887"},{"key":"e_1_2_8_6_1","volume-title":"Gephi: An open source software for exploring and manipulating networks. 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