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[[TableOfContents]] <<TableOfContents>>
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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://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://www.cytoscape.org|Cytoscape]] in Java. Freely available (open-source)
 * [[http://www.codeplex.com/nodexl|NodeXL]] in C#/.Net. Freely available (open-source) extension to Excel 2007 adds social network analysis and visualization features.
 * [[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
 * [[http://cgi.cse.unsw.edu.au/~wyos/skyrails/|Skyrails]] - Visualizing 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://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++ 		 * [[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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||raw data import ||delimited text, .mrna format ||affy, delimited-text || || ||TXT, Excel, CEL, GPR ||Spotfire, GeneSpring || || || || || ||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 || ||

Contents

  1. Software applications
  2. Programming Libraries
  3. Layouts
  4. Other link directories
  5. Network Visualization
  6. Competitive Landscape (Under Construction)

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

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 c-98-207-16-44)

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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