Help:Tutorial

From WikiPathways

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== Advanced tutorials ==
== Advanced tutorials ==
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* [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]]
=== WikiPathways and PathVisio ===
=== WikiPathways and PathVisio ===
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A set of brief tutorials and videos describing how to access WikiPathways from PathVisio, using the WikiPathways Client Plugin:
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A set of brief 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]  
* [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio]  
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A tutorial describing how to edit curate WikiPathways pathways in 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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=== Analyzing data with PathVisio ===
=== Analyzing data with PathVisio ===
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These tutorials show you how to use WikiPathways pathways in PathVisio.
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These tutorials show you how to use WikiPathways pathways in PathVisio for data analysis.
* [http://www.pathvisio.org/documentation/tutorials/tutorial-2/ Analyzing data in PathVisio]
* [http://www.pathvisio.org/documentation/tutorials/tutorial-2/ Analyzing data in PathVisio]
* [http://developers.pathvisio.org/wiki/MetabolomicsTutorial Analyzing metabolomics data in PathVisio]
* [http://developers.pathvisio.org/wiki/MetabolomicsTutorial Analyzing metabolomics data in PathVisio]

Revision as of 22:12, 12 January 2016


Video tutorial

The following pages show you step-by-step how to draw a simplified version of the Statin pathway.

Advanced tutorials

WikiPathways and PathVisio

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

Extend and layout pathways using 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, please see the Cytoscape Presentations. The following tutorials will show a few Cytoscape apps at work: WikiPathways, CyTargetLinker and Mosaic.

Analyzing data with PathVisio

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

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).
editor_screenshot.png
Screenshot 1: the editor applet
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