Help:Tutorial

From WikiPathways

This tutorial explains how to create a pathway on WikiPathways, using the circadian clock pathway as an example.

The circadian clock pathway

The circadian clock is a molecular mechanism that maintains the cell's 24-hour molecular rhythm by driving the rhythmic expression of a wide range of genes, involved in metabolism, physiology and behaviour. In this tutorial, you will draw a simplified version of the pathway, restricting to the mPer/mCry feedback loop.

Step by step guide to drawing the circadian clock pathway

The following pages show you step-by-step how to draw a simplified version of the circadian clock pathway as described in the section above.

• Step 1: Log in to WikiPathways
• Step 2: Creating a new pathway; Adding data nodes, interactions and reactions
• Step 3: 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:

• Search and browse WikiPathways from PathVisio

A tutorial describing how to edit curate WikiPathways pathways in 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, Agilent Literature Search, CyTargetLinker and Mosaic.

• Using WikiPathways in Cytoscape
• Extend a pathway with the Agilent Literature Search
• Extend a pathway with CyTargetLinker
• Cytoscape and the Mosaic app

Analyzing data with PathVisio

These tutorials show you how to use WikiPathways pathways in PathVisio.

• Analyzing data in PathVisio
• Analyzing metabolomics data 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).

Screenshot 1: the editor applet