Diff for "Welcome" - Cytoscape Wiki

Differences between revisions 59 and 67 (spanning 8 versions)

Cytoscape is an open source platform for network data integration, analysis, and visualization. (Read more about Cytoscape...)

About Cytoscape Wiki

This is a wiki for both Cytoscape users and developers. If you find problems, or have suggestions, please let us know.

How to Edit

To edit wiki pages, sign up for an account, then add yourself to the editor list.
Tips for editing
See all pages in this wiki

Quick Links

For Users

For Developers

Latest user manual for next release
code.cytoscape.org - Start page for core developers
Cytoscape Consortium GitHub Account
Javadoc
- Latest Release: 3.0.1
- Latest Development Version: 3.1.0-SNAPSHOT
cytoscape.js - JavaScript library for web applications

Using Cytoscape

Manuals

Developers

Cytoscape 3.x Development

Cytoscape 3.x Developer Resources

Past Discussion about Cytoscape Architecture

Cytoscape 2.x Development

Attension App Developers: Cytoscape 2.x Series is in Maintenance Mode

If you are planning to develop a new Cytoscape App, we strongly recommend to use Cytoscape 3.x series. Cytoscpae core team is working on Cytoscape 3.x code base only and no new features will be added to 2.x series.

Participate in Cytoscape Development
Building_Cytoscape
Plugin Developer's Documents
Future_Cytoscape_Features
RFC_Index: Request for Comment (RFC) Index Page
Core Development Pages
- Newly started Cytoscape 3 documentation
- Outdated Cytoscape 3.0 pages, partly describing the 3.0-development process
- Cytoscape_2.7
- Cytoscape_2.6
- Cytoscape_2.5
- Google Summer of Code 2009: Ideas page for our GSoC application
- CytoscapeRetreat2010
- Hackathon Oct '09
- Mini Retreat Jun '10

Testing Cytoscape

Master Test Plan

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-== Introduction ==

[[http://www.cytoscape.org|{{attachment:cy3logo.png|http://cytoscape.org}}]]
+{{attachment:cy3logo.png|http://cytoscape.org}}
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-[[http://www.cytoscape.org|Cytoscape]] is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
+[[http://www.cytoscape.org|Cytoscape]] is an open source platform for network data integration, analysis, and visualization.  ([[http://www.cytoscape.org/what_is_cytoscape.html|Read more about Cytoscape...]])
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+== About Cytoscape Wiki ==

This is a wiki for both Cytoscape users and developers.  If you find problems, or have suggestions, [[https://groups.google.com/forum/?fromgroups#!forum/cytoscape-discuss|please let us know]].



=== How to Edit ===
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+----



== Quick Links ==

=== For Users ===

 * [[http://www.cytoscape.org/|Cytoscape Web Site]]

 * [[http://apps.cytoscape.org/|Cytoscape App Store]]

 * [[http://www.cytoscape.org/releasenotes.html|Release Notes]]

 * [[https://speakerdeck.com/cytoscape|Presentation Slides]]



=== For Developers ===

 * [[Cytoscape_3/UserManual|Latest user manual for next release]]

 * [[http://code.cytoscape.org/|code.cytoscape.org]] - Start page for core developers

 * [[https://github.com/cytoscape|Cytoscape Consortium GitHub Account]]

 * Javadoc

    * [[http://chianti.ucsd.edu/cytoscape-3.0.1/API/|Latest Release: 3.0.1]]

    * [[https://code.cytoscape.org/jenkins/job/cytoscape-3-javadoc/lastBuild/javadoc/|Latest Development Version: 3.1.0-SNAPSHOT]]

 * [[http://cytoscape.github.io/cytoscape.js/|cytoscape.js]] - JavaScript library for web applications



----
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- * [[Cytoscape_User_Manual|User Manual]]: Development draft

 * [[Data_Sets|Exampledata sets]] to use in Cytoscape
+=== Manuals ===

 * [[http://cytoscape.org/manual/Cytoscape2_8Manual.html|2.x]]

 * [[http://www.cytoscape.org/manual/Cytoscape3_0_1Manual.pdf|3.x]]



 * [[http://wiki.cytoscape.org/Cytoscape_3/UserManual|Latest Manual (Wiki version)]]



=== Other Useful Links ===

 * Tutorials

    * [[http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3|3.x]]

    * [[http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape|2.x]]

    * [[InternationalConferenceOnSystemsBiologyDemos|2.x Recipes]] - Based on 2.x plugin development

    * [[Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook|3.x Cookbook]] - Based on 3.x app development
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- * [[InternationalConferenceOnSystemsBiologyDemos|Recipes]]: Use case based plugin tutorials
+ * [[Data_Sets|Example data sets]] to use in Cytoscape
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-== Cytoscape 3 User Documents ==

 * [[Cytoscape_3/UserManual|User Manual]]: 3.0.0 development draft
+== Developers ==
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-== Developing Cytoscape ==
+=== Cytoscape 3.x Development ===

 * [[Cytoscape_3|Cytoscape 3.x Developer Resources]]



=== Past Discussion about Cytoscape Architecture ===

 * [[Outdated_Cytoscape_3.0/Mini_Retreat2|Mini Retreat: March 4, 2011 at UCSD]]

 * [[Cytoscape_3/MiniRetreat2012|Mini Retreat: Feb. 23, 2012 at UCSD (Cytoscape 3 pre-release discussion)]]
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+{{{#!wiki caution

'''Attension App Developers: Cytoscape 2.x Series is in Maintenance Mode'''



If you are planning to develop a new Cytoscape App, we strongly recommend to use Cytoscape 3.x series.  

Cytoscpae core team is working on Cytoscape 3.x code base only and no new features will be added to 2.x series.

}}}
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-=== Cytoscape 3 Development ===

 * [[Cytoscape_3|Cytoscape 3.0 Development]]
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- * [[Outdated_Cytoscape_3.0/Mini_Retreat2|Mini Retreat: March 4, 2011 at UCSD]]

 * [[Cytoscape_3/MiniRetreat2012|Mini Retreat: Feb. 23, 2012 at UCSD (Cytoscape 3 pre-release discussion)]]



== Testing Cytoscape ==
+=== Testing Cytoscape ===