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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* [[Help:Tutorial:Step 2|Step 2: Create a new pathway]]
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* [[Help:Tutorial:Step 3|Step 3: The proteins of the circadian clock pathway]]
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* [[Help:Tutorial:Step 4|Step 4: Illustrate the E-box enhancer]]
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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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* [[Help:Tutorial:Step 11|Step 11: Adding a curation tag]]
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== Advanced tutorials ==
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=== Visualizing data on pathways in GenMAPP-CS ===
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This tutorial shows you how use WikiPathways to visualize experimental data with [http://www.genmapp.org/beta/genmappcs/ GenMAPP-CS].
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* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:ExpressionAnalysisGenMAPP-CS Expression Analysis in GenMAPP-CS]
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=== WikiPathways and PathVisio ===
=== WikiPathways and PathVisio ===
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A set of brief tutorials and videos describing how to access WikiPathways from PathVisio, using the WikiPathways Client Plugin:
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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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* [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio]  
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<!--* [http://plugins.pathvisio.org/wp-client/tutorials/ Search and browse WikiPathways from PathVisio] -->
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A tutorial describing how to edit curate WikiPathways pathways in PathVisio:
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* [[Help:WPClientPluginCuration|Editing pathways with the WikiPathways Client Plugin for PathVisio]]
* [[Help:WPClientPluginCuration|Editing pathways with the WikiPathways Client Plugin for PathVisio]]
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=== Extend and layout pathways using Cytoscape ===
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These tutorials show you how to use WikiPathways in PathVisio for data analysis.
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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 [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/agilentliteraturesearch Agilent Literature Search], [http://apps.cytoscape.org/apps/cytargetlinker CyTargetLinker] and [http://apps.cytoscape.org/apps/mosaic Mosaic].
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* [https://pathvisio.org/tutorials/visualization.html Data visualization in PathVisio]
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* [https://pathvisio.org/tutorials/multi-omics-tutorial.html Multi-omics data visualization with PathVisio]
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* [http://apps.cytoscape.org/apps/wikipathways Using WikiPathways in Cytoscape]
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* [[Help:Tutorial:Cytoscape and Agilent Literature Search|Extend a pathway with the Agilent Literature Search]]
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* [http://projects.bigcat.unimaas.nl/cytargetlinker/tutorial2/ Extend a pathway with CyTargetLinker]
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* [http://nrnb.org/tools/mosaic/#runningmosaic Cytoscape and the Mosaic app]
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=== Analyzing data with PathVisio ===
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These tutorials show you how to use WikiPathways pathways in PathVisio.
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* [http://www.pathvisio.org/documentation/tutorials/tutorial-2/ Analyzing data in PathVisio]
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* [http://developers.pathvisio.org/wiki/MetabolomicsTutorial Analyzing metabolomics data in PathVisio]
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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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=== WikiPathways and Cytoscape ===
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; Drawing area: The area on which the pathway is drawn (see screenshot 1A).
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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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; Property table: The table where you can edit properties of the currently selected object(s). The property
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* [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title Visualizing data on pathways in Cytoscape]
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table is located in the sidepanel under the tab named 'Properties'.  
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* [https://cytargetlinker.github.io/cytoscape-tutorials/presentations/cytargetlinker#/title CyTargetLinker App]
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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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* [[Help:PathwayStyling|Styling WikiPathways Models in Cytoscape]]
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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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|'''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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