Biological graph layout and display

Package	Credits	Institutions	Availability
Cytoscape	PIs: Trey Ideker, Benno Schwikowski, Chris Sander Developers: Paul Shannon, Owen Ozier, Andrew Markiel, Nada Amin, Jonathan Wang, Iliana Avila-Campillo, Gary Bader, Ethan Cerami, Larissa Kamenkovich, Chris Workman	Institute for Systems Biology, UC San Diego, Memorial Sloan-Kettering Cancer Center	Open source
Osprey	PI: Mike Tyers Developers: Bobby-Joe Breitkreutz, Chris Stark	Mount Sinai Hospital, University of Toronto	Free for academics
VCN	PI: Michael Levitt Grad student: Nizar Batada	Stanford University	Open source
VxInsight		VisiWave	Commercial

General purpose graph layout and display

Package	Credits	Institutions	Availability
aiSee		AbsInt	Commercial
neato	Emden Gansner, Stephen North	AT&T Research	Open source
Pajek	Vladimir Batagelj	University of Konstanz	Executable free for noncommercial use. Source unclear
yED		yWorks	Commercial. Executable free.