Help:Tutorial
From WikiPathways
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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]. | [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]. | ||
| - | * [ | + | * [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title Visualizing data on pathways in Cytoscape] |
* [[Help:PathwayStyling|Styling WikiPathways Models 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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Revision as of 19:24, 9 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.
