#acl BaderLabGroup:read,write,revert,delete All:

We can migrate some of the content from the MCODE site here:
http://cbio.mskcc.org/~bader/software/mcode/

attachment:MCODELogo.png

MCODE is a Cytoscape !PlugIn designed to aid in cluster discovery.  Clusters are deemed to be highly interconnected regions within a network. Depending on the type of network, clusters may mean different things. For instance, clustering of protein-protein interaction networks has been shown to produce protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.

MCODE is a relatively fast method of clustering, although it does not currently provide any statistical score on the resulting clusters. It can be used as discovery tool when analyzing a network. See the paper for more information.

[[TableOfContents()]]

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== Downloads ==

=== MCODE v1.2 ===
 * plugin
  * requires Cytoscape v2.3.2 or later
 * Javadoc

=== MCODE v1.1 ===
 * plugin
  * requires Cytoscape v2.1
 * Javadoc
 * Run using Java WebStart

=== MCODE v1.0 ===
 * plugin
  * requires Cytoscape v2.0

=== Cytoscape ===
 * Link to cytoscape page

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== User's Manual ==
=== Installation ===
=== Introduction ===
=== Advanced Techniques ===
=== Tutorials ===
=== Index ===

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== Future Developments ==

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== Contact ==

=== Bugs / Feature Requests ===
If you encounter a bug with this !PlugIn, or have a feature suggestion, please e-mail [:GaryBader: Gary Bader].  Be sure to take a look at the Future Developments section before e-mailing a feature request.

=== Collaboration ===
This software is open-source. If you modify the source code and would like the modification to be included in a subsequent release, I would love to hear from you. Please send me an e-mail to [:GaryBader: Gary Bader].

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== Acknowledgements ==

This software was originally released as a command-line-only program from the Hogue Lab.  It was created by [:GaryBader: Gary Bader], currently based in the [:Home:Bader Lab] at the University of Toronto (formerly in the Sander Group,[http://www.cbio.mskcc.org/  Computational Biology Center, Memorial Sloan-Kettering Cancer Center], New York City)

Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab.

This software is made available under the [http://www.gnu.org/copyleft/lesser.html LGPL] (Lesser General Public License), which means that you can freely use it within your own software, but if you alter the code itself and distribute it, you must make the source code alterations freely available as well.

Please see the following paper for more information about the algorithm:
 * Bader GD, Hogue CW.
 . An automated method for finding molecular complexes in large protein interaction networks.
 . ''BMC Bioinformatics''. 2003 Jan 13;4(1):2.
 . http://www.biomedcentral.com/1471-2105/4/2