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 that finds clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be 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()

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

User's Manual

Installation

Introduction

Advanced Techniques

Tutorials

Index

Future Developments

Contact

Bugs / Feature Requests

If you encounter a bug with this PlugIn, or have a feature suggestion, please e-mail GaryBader. 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.

Acknowledgements

This software was originally released as a command-line-only program from the Hogue Lab. It was created by Gary Bader, currently based in the [http://www.baderlab.org/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 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