Cytoscape

http://wiki.cytoscape.org/ScriptingPlugins

http://wiki.cytoscape.org/Cytoscape_User_Manual/Attributes

http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats

http://wiki.cytoscape.org/Cytoscape_User_Manual/Visual_Styles

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape#Force-Directed_Layout

Command line options from the user manual:

Cytoscape recognizes a number of optional command line arguments, including run-time specification of 
network files, attribute files, and session files. 
This is the output generated when the cytoscape is executed with the "-h" or "--help" flag:

usage: java -Xmx512M -jar cytoscape.jar [OPTIONS]
-h,--help 
-v,--version 
-s,--session <file> 
-N,--network <file> 
-e,--edge-attrs <file> 
-n,--node-attrs <file> 
-m,--matrix <file> 
-p,--plugin <file>
-P,--props <file> 
-V,--vizmap <file>

Cytoscape Web

http://cytoscapeweb.cytoscape.org/tutorial

Home