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__NOTOC__ __NOEDITSECTION__ == Introductory tutorial == The following pages show you step-by-step how to draw a simplified version of the Statin pathway. * [[Help:Tutorial:Step 1|Step 1: Log in to WikiPathways]] * [[Help:Tutorial:Step_2_v2|Step 2: Creating a new pathway: Adding data nodes, interactions and reactions]] * [[Help:Tutorial:Step_3_v2|Step 3: Completing the pathway: Adding compartments, labels, complexes; Illustrating transport and adding a literature reference]] * [[Help:Tutorial:Step_4_v2|Step 4: Adding a description and curation tag]] == Advanced tutorials == * [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]] ==== WikiPathways and PathVisio ==== A set of tutorials and videos describing how to access and edit WikiPathways from PathVisio, using the WikiPathways Client Plugin: * [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio] * [[Help:WPClientPluginCuration|Editing pathways with the WikiPathways Client Plugin for PathVisio]] ==== Extend and layout pathways using Cytoscape ==== [http://www.cytoscape.org Cytoscape] is a tool for network visualization and analysis. In the following tutorials we will highlight some of the Cytoscape functionality that is relevant for the pathways as used on WikiPathways. For tutorials of other Cytoscape features, please see the [https://speakerdeck.com/cytoscape Cytoscape Presentations]. The following tutorials will show a few Cytoscape apps at work: [http://apps.cytoscape.org/apps/wikipathways WikiPathways], [http://apps.cytoscape.org/apps/cytargetlinker CyTargetLinker] and [http://apps.cytoscape.org/apps/mosaic Mosaic]. * [http://apps.cytoscape.org/apps/wikipathways Using WikiPathways in Cytoscape] * [http://projects.bigcat.unimaas.nl/cytargetlinker/tutorial2/ Extend a pathway with CyTargetLinker] * [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app] ==== Analyzing data with PathVisio ==== These tutorials show you how to use WikiPathways in PathVisio for data analysis. * [http://www.pathvisio.org/documentation/tutorials/tutorial-2/ Analyzing data in PathVisio] * [http://developers.pathvisio.org/wiki/MetabolomicsTutorial Analyzing metabolomics data in PathVisio] == Commonly used terms == ; Sidepanel: The panel containing the ''Properties'' and ''Backpage'' tabs (see screenshot 1B). ; Drawing area: The area on which the pathway is drawn (see screenshot 1A). ; Property table: The table where you can edit properties of the currently selected object(s). The property table is located in the sidepanel under the tab named 'Properties'. ; Backpage browser: A panel that gives detailed annotation info on the currently selected DataNode. The Backpage browser is located in the sidepanel under the tab named 'Backpage'. ; Toolbar: see screenshot 1C. ; Infobox: Displays information about the pathway (see screenshot 1D). {|class=prettytable |{{TutorialImage|editor_screenshot.png}} |- |'''Screenshot 1: the editor applet''' |}

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