Help:Tutorial

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== Introductory tutorial ==
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= Introductory tutorial =
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The following pages show you step-by-step how to draw a simplified version of the Statin pathway.
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WikiPathways Academy will teach you everything you need to know to start contributing to WikiPathways, from how to create a WikiPathways account, how to use our editing tools, and how to make your pathway public at WikiPathways. The Academy is designed as a path, starting with basic terminology and rapidly progressing to using the authoring tools.  
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* [[Help:Tutorial:Step 1|Step 1: Log in to WikiPathways]]
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'''Access the Academy [https://wikipathways.github.io/academy/path.html here]!'''
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* [[Help:Tutorial:Step_2_v2|Step 2: Creating a new pathway: Adding data nodes, interactions and reactions]]
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* [[Help:Tutorial:Step_3_v2|Step 3: Completing the pathway: Adding compartments, labels, complexes; Illustrating transport and adding a literature reference]]
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* [[Help:Tutorial:Step_4_v2|Step 4: Adding a description and curation tag]]
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== Advanced tutorials ==
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= Advanced tutorials =
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* [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]]
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==== WikiPathways and PathVisio ====
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=== WikiPathways and PathVisio ===
A set of tutorials and videos describing how to access and edit WikiPathways from PathVisio, using the WikiPathways Client Plugin:
A set of tutorials and videos describing how to access and edit WikiPathways from PathVisio, using the WikiPathways Client Plugin:
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* [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio]  
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<!--* [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio] -->
* [[Help:WPClientPluginCuration|Editing pathways with the WikiPathways Client Plugin for PathVisio]]
* [[Help:WPClientPluginCuration|Editing pathways with the WikiPathways Client Plugin for PathVisio]]
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==== Extend and layout pathways using Cytoscape ====
 
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[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, visit [http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3 OpenTutorials]. 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].
 
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* [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]]
 
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* [http://projects.bigcat.unimaas.nl/cytargetlinker/tutorial2/ Extend a pathway with CyTargetLinker]
 
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* [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app]
 
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==== Analyzing data with PathVisio ====
 
These tutorials show you how to use WikiPathways in PathVisio for data analysis.
These tutorials show you how to use WikiPathways in PathVisio for data analysis.
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* [http://www.pathvisio.org/documentation/tutorials/tutorial-2/ Analyzing data in PathVisio]
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* [https://pathvisio.org/tutorials/visualization.html Data visualization in PathVisio]
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* [http://developers.pathvisio.org/wiki/MetabolomicsTutorial Analyzing metabolomics data in PathVisio]
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* [https://pathvisio.org/tutorials/multi-omics-tutorial.html Multi-omics data visualization with PathVisio]
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== Commonly used terms ==
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; Sidepanel: The panel containing the ''Properties'' and ''Backpage'' tabs (see screenshot 1B).
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=== WikiPathways and Cytoscape ===
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; Drawing area: The area on which the pathway is drawn (see screenshot 1A).
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[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, visit [https://github.com/cytoscape/cytoscape-tutorials/wiki Cytoscape Tutorials]. The following tutorials will show a few Cytoscape apps at work:
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; Property table: The table where you can edit properties of the currently selected object(s). The property
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* [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title Visualizing data on pathways in Cytoscape]
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table is located in the sidepanel under the tab named 'Properties'.  
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* [https://cytargetlinker.github.io/cytoscape-tutorials/presentations/cytargetlinker#/title CyTargetLinker App]
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; Backpage browser: A panel that gives detailed annotation info on the currently selected DataNode. The Backpage browser
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* [[Help:PathwayStyling|Styling WikiPathways Models in Cytoscape]]
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is located in the sidepanel under the tab named 'Backpage'.
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; Toolbar: see screenshot 1C.
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; Infobox: Displays information about the pathway (see screenshot 1D).
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{|class=prettytable
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|{{TutorialImage|editor_screenshot.png}}
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|-
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|'''Screenshot 1: the editor applet'''
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|}
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Current revision


Introductory tutorial

WikiPathways Academy will teach you everything you need to know to start contributing to WikiPathways, from how to create a WikiPathways account, how to use our editing tools, and how to make your pathway public at WikiPathways. The Academy is designed as a path, starting with basic terminology and rapidly progressing to using the authoring tools.

Access the Academy here!

Advanced tutorials

WikiPathways and PathVisio

A set of tutorials and videos describing how to access and edit WikiPathways from PathVisio, using the WikiPathways Client Plugin:

These tutorials show you how to use WikiPathways in PathVisio for data analysis.

WikiPathways and Cytoscape

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, visit Cytoscape Tutorials. The following tutorials will show a few Cytoscape apps at work:

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