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{{attachment:cy3logo.png|http://cytoscape.org}}

[[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...]])

== 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 ===
 * To edit wiki pages, ask an existing wiki user to create a name and temporary password for you at [[http://wiki.cytoscape.org/cgi-bin/moin.cgi/?action=newaccount|sign up for an account]], then ask the wiki user to add your new user name to the [[EditorGroup|editor list]]. Once this is complete, you can log in using your name and temporary password, then change your password. To edit a page, surf to the page and use the Edit button in the upper left corner.
 * [[Tips_on_using_this_wiki|Tips for editing]]
 * [[TitleIndex|See all pages in this wiki]]

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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://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder|App Ladder]] - Start page for app developers
 * [[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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== Using Cytoscape ==
=== Manuals ===
 * [[http://cytoscape.org/manual/Cytoscape2_8Manual.html|2.x]]
 * [[http://www.cytoscape.org/manual/Cytoscape3_0_1Manual.pdf|3.x]]

 * [[http://manual.cytoscape.org|Latest Manual]]

=== 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
 * [[Publications]] about Cytoscape
 * [[Presentations]] about Cytoscape

 * [[Data_Sets|Example data sets]] to use in Cytoscape
 * [[Network_analysis_links|Other network analysis links]]

== Developers ==

=== 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)]]

=== Cytoscape 2.x Development ===
{{{#!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.
}}}

 * [[Developer_Homepage|Participate in Cytoscape Development]]
 * [[Building_Cytoscape]]
 * [[cytoscape_developer_tutorial|Plugin Developer's Documents]]
 * [[Future_Cytoscape_Features]]
 * [[RFC_Index]]: Request for Comment (RFC) Index Page
 * [[Cytostaff_Development|Core Development Pages]] <<Include(Current_Dev_Items)>>


=== Testing Cytoscape ===
 * [[Master Test Plan]]