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:    cytoscape.sh
            *   On Windows, run:                  cytoscape.bat


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
      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