MultiLevelLayout Plugin for Cytoscape

Multilevel Layout Plug-In applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks.

Downloads

The Plug-In is available for download from the Downloads page.

Quick Start Guide

1. Download the Plug-In
2. Copy the downloaded Plug-In into Cytoscape's plugins directory
3. Start Cytoscape
4. Open an interaction network into Cytoscape
5. Start the Plug-In from the Cytoscape's Layout->Multilevel Layout menu
6. You can use the Plug-In with custom settings from the Layout->Settings... menu

Source codes

The source codes of the Plug-In are available from google codes svn and you can browse them in the Source page.

Citation

In case you will use the code or plugin in your work, we would appreciate a citation to the publication:

Tuikkala J, Vahamaa H, Salmela P, Nevalainen OS, Aittokallio T. A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. BioData Mining 2012; 5(1):2. http://www.biodatamining.org/content/5/1/2/