Help:Tutorial

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This tutorial explains how to create a pathway on WikiPathways, using the circadian clock pathway as an example.
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= Introductory tutorial =
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WikiPathways Academy will teach you everything you need to know to start contributing to WikiPathways, from how to create a WikiPathways account, how to use our editing tools, and how to make your pathway public at WikiPathways. The Academy is designed as a path, starting with basic terminology and rapidly progressing to using the authoring tools.  
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== The circadian clock pathway ==
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'''Access the Academy [https://wikipathways.github.io/academy/path.html here]!'''
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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.
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== Step by step guide to drawing the circadian clock pathway ==
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= Advanced tutorials =
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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.
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* [[Help:Tutorial:Step 1|Step 1: Log in to WikiPathways]]
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=== WikiPathways and PathVisio ===
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* [[Help:Tutorial:Step 2|Step 2: Create a new pathway]]
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A set of tutorials and videos describing how to access and edit WikiPathways from PathVisio, using the WikiPathways Client Plugin:
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* [[Help:Tutorial:Step 3|Step 3: The proteins of the circadian clock pathway]]
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<!--* [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio] -->
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* [[Help:Tutorial:Step 4|Step 4: Illustrate the E-box enhancer]]
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* [[Help:WPClientPluginCuration|Editing pathways with the WikiPathways Client Plugin for PathVisio]]
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* [[Help:Tutorial:Step 5|Step 5: Clock and Bmal1 dimerize and bind to the E-box element]]
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* [[Help:Tutorial:Step 6|Step 6: Target genes are activated by the E-box element]]
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* [[Help:Tutorial:Step 7|Step 7: The negative feedback loop]]
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* [[Help:Tutorial:Step 8|Step 8: Draw cellular locations]]
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* [[Help:Tutorial:Step 9|Step 9: Adding bibliography]]
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* [[Help:Tutorial:Step 10|Step 10: Adding a description]]
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== Advanced tutorials ==
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These tutorials show you how to use WikiPathways in PathVisio for data analysis.
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=== Use the circadian clock pathway in GenMAPP ===
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* [https://pathvisio.org/tutorials/visualization.html Data visualization in PathVisio]
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The next tutorial shows you how use the pathway you created to visualize experimental data with [http://www.genmapp.org GenMAPP].
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* [https://pathvisio.org/tutorials/multi-omics-tutorial.html Multi-omics data visualization with PathVisio]
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* [[Help:Tutorial:Visualize experimental data with GenMAPP|GenMAPP tutorial]]
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=== Extend and layout pathways using Cytoscape ===
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=== WikiPathways and Cytoscape ===
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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, 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].
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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 [https://github.com/cytoscape/cytoscape-tutorials/wiki Cytoscape Tutorials]. The following tutorials will show a few Cytoscape apps at work:
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* [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title Visualizing data on pathways in Cytoscape]
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* [[Help:Tutorial:Cytoscape and Agilent Literature Search|Cytocape and Agilent Literature Search]]
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* [https://cytargetlinker.github.io/cytoscape-tutorials/presentations/cytargetlinker#/title CyTargetLinker App]
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* [[Help:Tutorial:Using Cytoscape and Bubblerouter|Cytoscape and the Bubblerouter plugin]]
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* [[Help:PathwayStyling|Styling WikiPathways Models in Cytoscape]]
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== Commonly used terms ==
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; Sidepanel: The panel containing the ''Properties'' and ''Backpage'' tabs (see screenshot 1B).
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; Drawing area: The area on which the pathway is drawn (see screenshot 1A).
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; Property table: The table where you can edit properties of the currently selected object(s). The property
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table is located in the sidepanel under the tab named 'Properties'.
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; Backpage browser: A panel that gives detailed annotation info on the currently selected DataNode. The Backpage browser
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is located in the sidepanel under the tab named 'Backpage'.
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; Toolbar: see screenshot 1C.
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; Infobox: Displays information about the pathway (see screenshot 1D).
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{|class=prettytable
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|{{TutorialImage|editor_screenshot.png}}
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|-
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|'''Screenshot 1: the editor applet'''
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|}
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Current revision


Introductory tutorial

WikiPathways Academy will teach you everything you need to know to start contributing to WikiPathways, from how to create a WikiPathways account, how to use our editing tools, and how to make your pathway public at WikiPathways. The Academy is designed as a path, starting with basic terminology and rapidly progressing to using the authoring tools.

Access the Academy here!

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:

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 Cytoscape Tutorials. The following tutorials will show a few Cytoscape apps at work:

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