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/CytoscapeRetreat2008/Daniel?action=AttachFile&do=get&target=DanielAbel-Toronto-CyRetreat08-slides.pdf

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

GML

http://en.wikipedia.org/wiki/Graph_Modelling_Language