Cytoscape Wiki|
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||Free for Academic use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||NO ||NO ||NO ||NO ||NO ||<bgcolor="#33ff00">YES || ||Free for Commercial use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||NO ||NO ||NO ||NO ||NO ||<bgcolor="#33ff00">YES || ||Open Source ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||NO ||NO ||NO ||NO ||NO ||NO || ||nbr Curated Pathways || ||96? || || || || || || || || ||nbr species supported || ||11 || || || || || || || || ||User-defined Pathways ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||Inferred Pathways ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || || || || || ||Pathway overrepresentation analysis ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || || || || ||Gene Ontology overrepresentation ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || || || || ||Automated Graph Layout ||<bgcolor="#33ff00">YES || || || || || || || || || |
||Free for Academic use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#00ff00">YES ||<bgcolor="#33ff00">YES || ||Free for Commercial use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#33ff00">YES || ||Open Source ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO || ||nbr Curated Pathways ||<bgcolor="#00ff00">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 ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||Inferred Pathways ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES || || ||Pathway overrepresentation analysis ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || ||Gene Ontology overrepresentation ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || ||Automated Graph Layout ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || || ||<bgcolor="#00ff00">YES ||YES || |
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||Graphical Overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES || || || || || ||User-defined overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || || || || ||SQL defined coloring criteria || ||<bgcolor="#33ff00">YES || || || || || || || || ||Multiple visual styles ||<bgcolor="#33ff00">YES || || || || || || || || || ||advance search/filter ||<bgcolor="#33ff00">YES || || || || || || || || || ||customizable gene/protein database || ||<bgcolor="#33ff00">YES || || || || || || || ||nbr input/output spigots || || || || || || || || || || ||statistical network analysis || || || || || || || ||<bgcolor="#33ff00">YES || || ||quantitative simulation || || || || ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || |
||Graphical Overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES ||YES || ||User-defined overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES || || ||SQL defined coloring criteria ||<bgcolor="#00ff00">in GenMAPP ||<bgcolor="#33ff00">YES || || || || || || || || ||Multiple visual styles ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES || || || || || || ||advance search/filter ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || ||customizable gene/protein database ||<bgcolor="#00ff00">in GenMAPP ||<bgcolor="#33ff00">YES || || || || ||<bgcolor="#33ff00">YES || || ||rich graphical annotation ||<bgcolor="#00ff00">in GenMAPP ||<bgcolor="#33ff00">YES || || || || || || || || ||nbr input/output spigots ||15 ||?? || ||12 ||16 || ||many ||4 ||16 || ||layers ||<bgcolor="#ff0000">coming || || || || || || ||<bgcolor="#00ff00">YES || || ||statistical network analysis ||<bgcolor="#33ff00">plugins || || ||shortest path || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||scripting, macros ||<bgcolor="#ff0000">NO || || || || || || ||<bgcolor="#33ff00">YES || || ||quantitative simulation ||<bgcolor="#ff0000">NO || || || ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || |
Software applications
[http://www.cytoscape.org Cytoscape] in Java. Freely available (open-source)
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16417636&query_hl=2&itool=pubmed_docsum GenoLink]. Free executable for academic use.
[http://ondex.sourceforge.net ONDEX]. Open source.
[http://nwb.slis.indiana.edu/ Network Workbench] A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research
[http://visant.bu.edu/ VisANT] - Java biological analysis software
[http://www.graphviz.org/ Graphviz] - Graph Visualization Software
[http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek] - Graph visualization and analysis software. Popular among social science community.
[http://biodata.mshri.on.ca/osprey/servlet/Index OSPREY] - Biological network visualization software.
[http://www.analytictech.com/ucinet/ucinet.htm UCINET] - De facto standard network analysis tool in social science. (commercial software)
Programming Libraries
[http://www.cytoscape.org Cytoscape] in Java. Freely available (open-source)
[https://networkx.lanl.gov/ NetworkX] in Python
[http://sbi.imim.es/piana/ PIANA] in Python. Freely available (open-source). Outputs results in Cytoscape 'importable' format (ie. sif, noa, eda).
[http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/graph.html Bioconductor graph package] in R. Freely available (open-source)
[http://www.jgraph.com/ JGraph] - Java Graph Visualization and Layout
[http://www.yworks.com/en/products_yfiles_about.htm yFiles] - Java Graph Layout and Visualization Library
[http://jgrapht.sourceforge.net/ JGraphT] - Java graph library
[http://jung.sourceforge.net/team.html JUNG] - Java Universal Network/Graph Framework
[http://medcd.iab.keio.ac.jp/expanda/ eXpanda] - Perl library for network visualization and analysis. (can import Cytoscape sif files.)
Layouts
[http://apropos.icmb.utexas.edu/lgl/ LGL] - Large Graph Layout
[http://www-sst.informatik.tu-cottbus.de/~an/GD/index.html#Downloads LinLogLayout]
[http://www.touchGraph.com/ Touchgraph] and [http://sourceforge.net/projects/touchgraph TouchGraph]
Other link directories
Network Visualization
Competitive Landscape
Feature |
Cytoscape |
GenMAPP |
Pathway Commons |
Jubilant |
Ariadne |
Ingenuity |
GeneGo |
pajek |
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 |
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500 |
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39 models in biomodels.net + cellml, DOQCS, PathArt |
nbr species supported |
GenMAPP, PC |
11 |
10 |
17 |
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User-defined Pathways |
YES |
YES |
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YES |
YES |
YES |
YES |
YES |
Inferred Pathways |
YES |
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YES |
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YES |
YES |
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Pathway overrepresentation analysis |
YES |
YES |
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YES |
YES |
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Gene Ontology overrepresentation |
YES |
YES |
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YES |
YES |
YES |
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Automated Graph Layout |
YES |
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YES |
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YES |
YES |
Interactive Graph Layout |
YES |
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Graphical Overlays |
YES |
YES |
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YES |
YES |
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YES |
YES |
YES |
User-defined overlays |
YES |
YES |
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YES |
YES |
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YES |
YES |
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SQL defined coloring criteria |
in GenMAPP |
YES |
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Multiple visual styles |
YES |
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YES |
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advance search/filter |
YES |
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YES |
YES |
YES |
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customizable gene/protein database |
in GenMAPP |
YES |
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YES |
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rich graphical annotation |
in GenMAPP |
YES |
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nbr input/output spigots |
15 |
?? |
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12 |
16 |
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many |
4 |
16 |
layers |
coming |
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YES |
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statistical network analysis |
plugins |
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shortest path |
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YES |
YES |
YES |
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scripting, macros |
NO |
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YES |
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quantitative simulation |
NO |
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YES |
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YES |