Cytoscape WikiContents
Software applications
Cytoscape in Java. Freely available (open-source)
NodeXL in C#/.Net. Freely available (open-source) extension to Excel 2007 adds social network analysis and visualization features.
GenoLink. Free executable for academic use.
ONDEX. Open source.
Network Workbench A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research
VisANT - Java biological analysis software
Graphviz - Graph Visualization Software
Pajek - Graph visualization and analysis software. Popular among social science community.
OSPREY - Biological network visualization software.
UCINET - De facto standard network analysis tool in social science. (commercial software)
Vizster - Social network visualization software
WilmaScope - Java3D application which creates real time 3d animations of dynamic graph structures.
NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto
BioLayout Express3D - 3D Java graph visualization
Walrus - Java3D directed graph visualization
ProViz - protein interaction network visualization tool built using TULIP C++ graph library
PIMWalker - Java based PSI-MI protein interaction network visualizer
GUESS - Java graph exploration system
InFlow - Commercial Software for Social Network Analysis & Organizational Network Analysis
NetMiner - Commercial social network analysis software
GraphExplore - Free Java network visualizer
Chisio - Compound or Hierarchical Graph Visualization Tool
Gephi - graph exploration and manipulation software
Arena3D - Visualizing biological networks in 3D
Skyrails - Visualizing networks in 3D
Programming Libraries
Cytoscape in Java. Freely available (open-source)
NetworkX in Python
PIANA in Python. Freely available (open-source). Outputs results in Cytoscape 'importable' format (ie. sif, noa, eda).
Bioconductor graph package in R. Freely available (open-source)
JGraph - Java Graph Visualization and Layout
yFiles - Java Graph Layout and Visualization Library
JGraphT - Java graph library
JUNG - Java Universal Network/Graph Framework
eXpanda - Perl library for network visualization and analysis. (can import Cytoscape sif files.)
Prefuse - Interactive information visualization library
OpenJgraph - Java graph layout
Layouts
LGL - Large Graph Layout
Touchgraph and TouchGraph
Boost graph library in C++
LEDA - graph algorithm library in C++
TULIP - graph library in C++
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" |
|
|
|
|
|
|
|
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Embedded SQL database |
|
|
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relevance networks |
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