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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 find clusters in large networks.  Clusters are deemed to be more highly interconnected regions within the network and depending on the nature of the network, they may mean different things. For instance, clustering of protein-protein interaction networks has been shown to produce protein complexes and parts of pathways while clusters in protein similarity networks represent protein families.

MCODE is a relatively fast method of clustering.  With an intuitive interface, it is suited for both computationally and biologically oriented reserachers.  MCODE allows the user to:
 * fine-tune numerous node-scoring and cluster-finding parameters
 * explore clusters interactively with real-time results
  * manipulate cluster size
  * visualize results logically with conservative layouter 
  * enumerate the clusters' node attributes for functional consistancy
 * manage multiple result sets
 * Output results
  * generate sub-networks from clusters
  * export results as text for spreadsheet purposes
Currently, MCODE does not provide any statistical score on the resulting clusters but can be used as a discovery tool in network analysis. Please see the [http://www.biomedcentral.com/1471-2105/4/2 MCODE 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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== Literature and Resources ==

=== MCODE Publication ===
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

=== User's Manual ===
The User's Manual includes installation instructions, explanations, examples and tutorials.  It is available [:Software/MCODE/UsersManual: here].

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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.