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= MCODE User's Manual =

[[TableOfContents()]]

== Installation ==
To use the MCODE PlugIn, you must first obtain a copy of Cytoscape.  The corresponding MCODE and Cytoscape versions are outlined in the downloads section on the MCODE website.  The lastest MCODE, version 1.2, requires Cytoscape 2.3.2 or later.
 * You can download a copy of Cytoscape 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.
 1. Start Cytoscape. For example, on Unix/Linux or MacOS X, run:
cytoscape.sh

On Windows, run:
cytoscape.bat

''''You may also load the plugin via the Plugin menu in Cytoscape.'''' IS THIS TRUE?

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== Running MCODE ==
MCODE is an extension for Cytoscape and can only be accessed through Cytoscape.
 1. Start Cytoscape
 1. Go to the Plugins Menu
 1. Move the mouse over MCODE
 1. Click Start MCODE
  * The main MCODE interface will appear in the left panel of Cytoscape
Note: If MCODE does not appear in the Plugins Menu, then the installation of MCODE was not successfull. Please refer to the previous section of the User's Manual.

This menu provides two additional options:
 * About MCODE
  * A quick reference to MCODE acknowledgements, citation information, and a link to the MCODE paper.
 * Help
  * A link that will open the MCODE website at www.baderlab.org in your default browser for quick access to downloads, contact information, and the User's Manual with help and tutorials.
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== Getting Results ==

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== Fine-Tuning Results ==
=== Scoring Parameters ===
=== Finding Parameters ===
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== Exploring Results ==
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== Outputting Results ==
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== Tutorials ==
=== BiNGO Validation ===
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