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* [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) * [http://jheer.org/vizster/ Vizster] - Social network visualization software * [http://wilma.sourceforge.net/ WilmaScope] - Java3D application which creates real time 3d animations of dynamic graph structures. |
* [[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) * [[http://jheer.org/vizster/|Vizster]] - Social network visualization software * [[http://wilma.sourceforge.net/|WilmaScope]] - Java3D application which creates real time 3d animations of dynamic graph structures. * [[http://ophid.utoronto.ca/navigator/|NAViGaTOR]] - Network Analysis, Visualization, & Graphing TORonto * [[http://www.sanger.ac.uk/Teams/Team101/biolayout/b3d.html|BioLayout Express3D]] - 3D Java graph visualization * [[http://www.caida.org/tools/visualization/walrus/|Walrus]] - Java3D directed graph visualization * [[http://cbi.labri.fr/eng/proviz.htm|ProViz]] - protein interaction network visualization tool built using TULIP C++ graph library * [[http://pim.hybrigenics.fr/pimriderext/pimwalker/index.html|PIMWalker]] - Java based PSI-MI protein interaction network visualizer * [[http://graphexploration.cond.org/|GUESS]] - Java graph exploration system * [[http://www.orgnet.com/|InFlow]] - Commercial Software for Social Network Analysis & Organizational Network Analysis * [[http://www.netminer.com|NetMiner]] - Commercial social network analysis software * [[http://graphexplore.cagp.duke.edu/|GraphExplore]] - Free Java network visualizer * [[http://www.cs.bilkent.edu.tr/~ivis/chisio.html|Chisio]] - Compound or Hierarchical Graph Visualization Tool * [[http://gephi.org/|Gephi]] - graph exploration and manipulation software * [[http://arena3d.org/index.html|Arena3D]] - Visualizing biological networks in 3D |
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* [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.) * [http://prefuse.org/ Prefuse] - Interactive information visualization library * [http://openjgraph.sourceforge.net/ OpenJgraph] - Java graph layout |
* [[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.) * [[http://prefuse.org/|Prefuse]] - Interactive information visualization library * [[http://openjgraph.sourceforge.net/|OpenJgraph]] - Java graph layout |
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* [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] |
* [[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]] * [[http://www.boost.org/libs/graph/doc/index.html|Boost]] graph library in C++ * [[http://www.algorithmic-solutions.com/enleda.htm|LEDA]] - graph algorithm library in C++ * [[http://www.labri.fr/perso/auber/projects/tulip/news.php|TULIP]] - graph library in C++ |
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= Competitive Landscape = ||'''Feature''' ||'''Cytoscape''' ||'''Gen''''''MAPP''' ||'''Pathway Commons''' ||'''Jubilant''' ||'''Ariadne''' ||'''Ingenuity''' ||'''Gene''''''Go''' ||'''pajek''' ||'''Cell''''''Designer''' || ||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, Path''''''Art || ||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 ||<bgcolor="#00ff00">YES || ||Interactive Graph Layout ||<bgcolor="#33ff00">YES || || || || || || || || || ||Graphical Overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES ||<bgcolor="#00ff00">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">via Mi''''''Ms? || || || ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || |
= Competitive Landscape (Under Construction) = ||'''Feature''' ||'''Cytoscape''' ||'''Gen''''''MAPP''' ||'''Pathway Commons''' ||'''Jubilant''' ||'''Ariadne''' ||'''Ingenuity''' ||'''Gene''''''Go''' ||'''pajek''' ||Visant ||'''Cell''''''Designer''' || ||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="#00ff00"> ||<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="#ff3333"> ||<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"> ||<bgcolor="#ff3333">NO || ||nbr Curated Pathways ||<bgcolor="#00ff00">GenMAPP, PC ||96? ||949 ||2100 || || ||500 || || ||39 models in biomodels.net + cellml, DOQCS, Path''''''Art || ||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"> ||<bgcolor="#33ff00">YES || ||Inferred Pathways ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES ||<bgcolor="#00ff00"> || || ||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 ||<bgcolor="#00ff00"> ||<bgcolor="#00ff00">YES || ||Interactive Graph Layout ||<bgcolor="#33ff00">YES || || || || || || || || || || ||Graphical Overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES ||<bgcolor="#00ff00"> ||<bgcolor="#00ff00">YES || ||User-defined overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#00ff00">YES ||<bgcolor="#00ff00"> || || ||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 || ||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 ||<bgcolor="#ff0000">coming || || || || || || ||<bgcolor="#00ff00">YES ||<bgcolor="#00ff00"> || || ||statistical network analysis ||<bgcolor="#33ff00">plugins || || ||shortest path || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00"> || || ||scripting, macros ||<bgcolor="#ff0000">NO || || || || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00"> || || ||quantitative simulation ||<bgcolor="#ff0000">via Mi''''''Ms? || || || ||<bgcolor="#33ff00">YES || || || || ||<bgcolor="#33ff00">YES || ||charting || || || || || || || || || || || ||"Enterprise Configuration" || || || || || || || || || || || ||Embedded SQL database || || || || || || || || || || || ||relevance networks || || || || || || || || || || || |
Contents
Software applications
Cytoscape in Java. Freely available (open-source)
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
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" |
|
|
|
|
|
|
|
|
|
|
Embedded SQL database |
|
|
|
|
|
|
|
|
|
|
relevance networks |
|
|
|
|
|
|
|
|
|
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