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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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----
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== Using Cytoscape ==
 * [[Cytoscape_User_Manual|User Manual]]: Development draft
 * [[Data_Sets|Exampledata sets]] to use in Cytoscape
== 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 ===
 * [[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

----

== Useing Cytoscape ==
=== Manuals ===
 * [[http://cytoscape.org/manual/Cytoscape2_8Manual.html|2.x]]
 * [[http://www.cytoscape.org/manual/Cytoscape3_0_1Manual.pdf|3.x]]

=== 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|Recipes]] - Use case based plugin tutorials
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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
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== Developing Cytoscape == == 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)]]
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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 ===

http://cytoscape.org

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


For Users

For Developers


Useing Cytoscape

Manuals

Developers

Cytoscape 3.x Development

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.

Testing Cytoscape

Welcome (last edited 2016-04-26 22:30:33 by server2)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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