Help:Tutorial
From WikiPathways
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=== Use the circadian clock pathway in GenMAPP === | === Use the circadian clock pathway in GenMAPP === | ||
The next tutorial shows you how use the pathway you created to visualize experimental data with [http://www.genmapp.org GenMAPP]. | The next tutorial shows you how use the pathway you created to visualize experimental data with [http://www.genmapp.org GenMAPP]. | ||
| - | * | + | * [[Help:Tutorial:Visualize experimental data with GenMAPP|GenMAPP tutorial]] |
=== 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 [http://cytoscape.org/cgi-bin/moin.cgi/Presentations Cytoscape wiki]. The following tutorials will show two plugins at work, the [http://cytoscape.org/cgi-bin/moin.cgi/Presentations/05_Literature Agilent Literature Search plugin] and the [http://www.genmapp.org/BubbleRouter/manual.htm Bubblerouter plugin]. | [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 [http://cytoscape.org/cgi-bin/moin.cgi/Presentations Cytoscape wiki]. The following tutorials will show two plugins at work, the [http://cytoscape.org/cgi-bin/moin.cgi/Presentations/05_Literature Agilent Literature Search plugin] and the [http://www.genmapp.org/BubbleRouter/manual.htm Bubblerouter plugin]. | ||
| - | * | + | * [[Help:Tutorial:Cytoscape and Agilent Literature Search|Cytocape and Agilent Literature Search]] |
| - | * | + | * [[Help:Tutorial:Using Cytoscape and Bubblerouter|Cytoscape and the Bubblerouter plugin]] |
== Commonly used terms == | == Commonly used terms == | ||
Revision as of 11:40, 17 April 2008
This tutorial explains you how to create a pathway on WikiPathways, using the Circadian clock pathway as 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: Create a new pathway
- Step 3: The proteins of the circadian clock pathway
- Step 4: Illustrate the E-box enhancer
- Step 5: Clock and Bmal1 dimerize and bind to the E-box element
- Step 6: Target genes are activated by the E-box element
- Step 7: The negative feedback loop
- Step 8: Draw cellular locations
- Step 9: Adding bibliography
- Step 10: Adding a description
Advanced tutorials
Use the circadian clock pathway in GenMAPP
The next tutorial shows you how use the pathway you created to visualize experimental data with GenMAPP.
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 wiki. The following tutorials will show two plugins at work, the Agilent Literature Search plugin and the Bubblerouter plugin.
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 |
