MCODE User's Manual
Installation
To use the MCODE PlugIn, you must first obtain a copy of Cytoscape. The compatible 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:
- Copy the MCODE.jar file to your [Cytoscape_Home]/plugins directory.
- Start Cytoscape. For example
- On Unix/Linux or MacOS X, run: cytoscape.sh
- On Windows, run: cytoscape.bat
- Check that MCODE appears in the Plugins menu of Cytoscape
- If it does not, then you likely placed the MCODE.jar file in the wrong directory. Repeat step one. You will have to restart Cytoscape to reload the plugin.
Running MCODE
MCODE is an extension for Cytoscape and can only be accessed through Cytoscape.
- Start Cytoscape
- Go to the Plugins Menu
- Move the mouse over MCODE
- 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.
Getting Results
Fine-Tuning Results
Scoring Parameters
Finding Parameters
Exploring Results
Outputting Results
Tutorials
BiNGO Validation