Third, users can search for an app based on its name, description, categories, authors and authors’ institutions. An app can belong to several categories, each chosen by their authors. Users find all apps of a given type by clicking on a category. Second, there is a list of categories for users with a general idea of the kind of app in which they are interested. Thus, we promote a learning-by-action approach to understanding the role and scope of apps by maintaining a low barrier to entry. First, we provide a Featured Apps section that invites new users of Cytoscape to simply click on a featured app, read about it and, with a single click, install it. The App Store offers multiple ways for users to discover apps ( Fig. Users can rate, review and perform one-click installation from their browser 2 METHODS ( B) A Cytoscape app page, where users can learn about the app through screenshots, a description and tutorial and Web site links. ( A) The Cytoscape App Store main page, with three ways for discovering apps: Featured Apps, Categories and Search. Here, we describe the features of the App Store for both users and app developers. The overarching goals of the Cytoscape App Store are to highlight the important features apps add to Cytoscape, to enable researchers to find apps they need and for developers to promote their apps. 1A) to coincide with the release of Cytoscape 3.0, a major re-architecturing of Cytoscape for improved stability, performance and versatility. To help address the needs of users, we launched the Cytoscape App Store ( Fig. Moreover, when users did find an interesting app through the web page catalog, they had to search for the app again in Cytoscape to install it. This catalog did not make it easy for users to discover apps in which they might be interested, e.g. Each app entry in the catalog listed all versions of an app and did not emphasize the latest version. Search was limited to exact matches to app names users could not search by app description, category or author and apps were categorized by single terms chosen by the Cytoscape team, not app developers. Originally, the Cytoscape team maintained a catalog of submitted apps (called ‘plugins’ at the time) that were accessible from a web page or from within Cytoscape. Over 150 free apps have been contributed to our Web site by developers from over a dozen countries. The wide-ranging functionality and specialization of Cytoscape principally reside in its apps. Cytoscape apps are additional software packages independently developed, licensed and installed. In addition, Cytoscape has an open architecture so that others can extend its functionality with apps. When users first install Cytoscape, it has a small well-defined set of functionality for working with networks. GUI Tutorials CyTargetLinker v.4.0+ (Cytoscape 3.6.+) TutorialĮxtend a set of microRNAs with regulatory informationĮxtend a biological pathway from WikiPathways with regulatory informationĮxtend a STRING protein-protein interaction network with pathway associationsĪPI Tutorials CyTargetLinker v.4.0+ (Cytoscape 3.6.Cytoscape is an open source software tool for network visualization and analysis, primarily for biological data ( Cline et al., 2007 Shannon et al., 2003). You can also have a look at our CyTargetLinker tutorial presentation to get started. Please have a look at our tutorials to get a better understanding on how CyTargetLinker works. | CyTargetLinker website and tutorials CyTargetLinker - Extend your biological networks in Cytoscape Home Documentation Tutorials Link sets Contact
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