MCODE PlugIn v1.2 ================= I. Introduction -----------This directory contains a copy of the MCODE PlugIn.

This PlugIn enables Cytoscape to cluster a network. The current release includes support for basic clustering of the network with many parameter customizations and interactive result exploration. This software is made available under the LGPL (Lesser General Public License). II. Resources --------MCODE website: http://www.baderlab.org/Software/MCODE * Latest updates as well as previous version downloads * Future developments * Links to Javadoc and source for developers Documentation: http://www.baderlab.org/Software/MCODE/UsersManual * Guide, Reference, and Tutorials MCODE Publication: http://www.biomedcentral.com/1471-2105/4/2 * Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003 Jan 13;4(1):2. * Abstract: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve &db=PubMed&list_uids=12525261&dopt=Abstract III. Installation Instructions ------------------------To use the MCODE PlugIn, you must first obtain a copy of Cytoscape, Version 2.3 or later. You can download a copy from: http://www.cytsoscape.org. Once you have downloaded Cytoscape and verified that it works, proceed with the next steps. 1. Copy the MCODE.jar file to your [Cytoscape_Home]/plugins directory. 2. Start Cytoscape. For example: * on Unix/Linux or MacOS X, run: * On Windows, run: IV. Bugs / Feature Requests ----------------------If you encounter a bug with this PlugIn, or have a feature suggestion, please e-mail Gary Bader (details below). Please look at the Future Developments at the MCODE website before e-mailing a cytoscape.sh cytoscape.bat

feature request. This software is open-source. If you modify the source code and would like the modification to be included in a subsequent release, e-mail a pre-built JAR file for evaluation of the feature. If the feature is deemed suitable for inclusion, a source code patch will be requested. V. Credits ------Version 1.2 was produced by Vuk Pavlovic in the Bader Lab. Thanks to Christopher Workman (The Technical University of Denmark) and Carlo Laudanna (University of Verona) for their expert input during beta-testing. 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 Bader Lab at the University of Toronto (formerly in the Sander Group, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York City) This software is made available under the 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. VI. Contacts -------Bader Lab, University of Toronto http://www.baderlab.org/ Sander Group, Computational Biology Center Memorial Sloan-Kettering Cancer Center, New York City http://www.cbio.mskcc.org/ For any questions concerning this PlugIn, please contact: Gary Bader: gary.bader AT utoronto.ca