Help:Tutorial
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=== 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://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://apps.cytoscape.org/apps/wikipathways Using WikiPathways in Cytoscape] | * [http://apps.cytoscape.org/apps/wikipathways Using WikiPathways in Cytoscape] | ||
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* [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] | ||
Revision as of 20:12, 5 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 brief tutorials and videos describing how to access WikiPathways from PathVisio, using the WikiPathways Client Plugin:
A tutorial describing how to edit curate WikiPathways pathways in 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.
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).
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| Screenshot 1: the editor applet |
