User:Jarle Pahr/Cytoscape
Le DH, Kwon YK. NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks. Bioinformatics 2011b;27:2767-2768.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0043287
Flux visualization:
http://sourceforge.net/projects/fluxvizplugin/?source=directory
Cytoscape 3 manual:
http://www.cytoscape.org/manual/Cytoscape3_0_1Manual.pdf
http://wiki.cytoscape.org/Cytoscape_3/UserManual
Undirected edges:
http://wiki.cytoscape.org/DanielAbel/EdgeDirectionality
Tutorials
http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape
http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3
File formats
http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats