Software applications

Programming Libraries

Layouts

Other link directories

Network Visualization

Competitive Landscape (Under Construction)

Feature

Cytoscape

GenMAPP

Pathway Commons

Jubilant

Ariadne

Ingenuity

GeneGo

pajek

Visant

CellDesigner

Free for Academic use

YES

YES

YES

NO

NO

NO

NO

YES

YES

Free for Commercial use

YES

YES

YES

NO

NO

NO

NO

NO

YES

Open Source

YES

YES

YES

NO

NO

NO

NO

NO

NO

nbr Curated Pathways

GenMAPP, PC

96?

949

2100

500

39 models in biomodels.net + cellml, DOQCS, PathArt

nbr species supported

GenMAPP, PC

11

10

17

User-defined Pathways

YES

YES

YES

YES

YES

YES

YES

Inferred Pathways

YES

YES

YES

YES

Pathway overrepresentation analysis

YES

YES

YES

YES

Gene Ontology overrepresentation

YES

YES

YES

YES

YES

Automated Graph Layout

YES

YES

YES

YES

Interactive Graph Layout

YES

Graphical Overlays

YES

YES

YES

YES

YES

YES

YES

User-defined overlays

YES

YES

YES

YES

YES

YES

SQL defined coloring criteria

in GenMAPP

YES

Multiple visual styles

YES

YES

advance search/filter

YES

YES

YES

YES

customizable gene/protein database

in GenMAPP

YES

YES

rich graphical annotation

in GenMAPP

YES

nbr input/output spigots

15

??

12

16

many

4

16

raw data import

delimited text, .mrna format

affy, delimited-text

TXT, Excel, CEL, GPR

Spotfire, GeneSpring

Affy, Agilent, Illumina, GE, ResolverTM , GeneSpringTM , Spotfire’s Decision Site TM, ArrayTrack, GeneData’s Expressionist and Phylosopher products, Inforsense’s KDE, SciTegic’s Pipeline Pilot, XenobaseResolver

MS Access, SPSS, Excel

GEO, tab-delimited text

layers

coming

YES

statistical network analysis

plugins

shortest path

YES

YES

YES

scripting, macros

NO

YES

quantitative simulation

via MiMs?

YES

YES

charting

"Enterprise Configuration"

Embedded SQL database

relevance networks

Network_analysis_links (last edited 2009-09-06 11:30:19 by Marc A. Smith)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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