Help:Tutorial
From WikiPathways
(Difference between revisions)
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* [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]] | * [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]] | ||
| - | === WikiPathways and PathVisio === | + | ==== WikiPathways and PathVisio ==== |
| - | A set of | + | 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] | * [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]] | ||
| - | === Extend and layout pathways using Cytoscape === | + | ==== 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://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]. | ||
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* [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app] | * [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app] | ||
| - | === Analyzing data with PathVisio === | + | ==== Analyzing data with PathVisio ==== |
These tutorials show you how to use WikiPathways pathways in PathVisio for data analysis. | 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] | ||
Revision as of 22:13, 12 January 2016
Video tutorial
The following pages show you step-by-step how to draw a simplified version of the Statin pathway.
- Step 1: Log in to WikiPathways
- Step 2: Creating a new pathway: Adding data nodes, interactions and reactions
- Step 3: Completing the pathway: Adding compartments, labels, complexes; Illustrating transport and adding a literature reference
- Step 4: Adding a description and curation tag
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:
- Search and browse WikiPathways from PathVisio
- Editing pathways with the WikiPathways Client Plugin for PathVisio
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).
|
| Screenshot 1: the editor applet |
