Help:Tutorial
From WikiPathways
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The following pages show you step-by-step how to draw a simplified version of the Statin pathway. | The following pages show you step-by-step how to draw a simplified version of the Statin pathway. | ||
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* [[Help:Tutorial:Step_4_v2|Step 4: Adding a description and curation tag]] | * [[Help:Tutorial:Step_4_v2|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: | 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]] | ||
| - | === | + | 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] | ||
| + | |||
| + | === WikiPathways and 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, 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]. | [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]. | ||
* [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]] | * [[Help:DataVisualizationInCytoscape|Visualizing data on pathways in Cytoscape]] | ||
| + | * [[Help:PathwayStyling|Styling WikiPathways Models in Cytoscape]] | ||
* [http://projects.bigcat.unimaas.nl/cytargetlinker/tutorial2/ Extend a pathway with CyTargetLinker] | * [http://projects.bigcat.unimaas.nl/cytargetlinker/tutorial2/ Extend a pathway with CyTargetLinker] | ||
* [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app] | * [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app] | ||
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== Commonly used terms == | == Commonly used terms == | ||
Revision as of 22:55, 7 November 2018
Introductory 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
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 OpenTutorials. The following tutorials will show a few Cytoscape apps at work: WikiPathways, CyTargetLinker and Mosaic.
- Visualizing data on pathways in Cytoscape
- Styling WikiPathways Models in Cytoscape
- Extend a pathway with CyTargetLinker
- Cytoscape and the Mosaic app
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 |
