From WikiPathways

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.

• Analyzing data in PathVisio
• Analyzing metabolomics data in PathVisio

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