Differences between revisions 52 and 67 (spanning 15 versions)

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)
[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

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.)
[http://prefuse.org/ Prefuse] - Interactive information visualization library
[http://openjgraph.sourceforge.net/ OpenJgraph] - Java graph layout

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]
[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++

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
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

-  ← Revision 52 as of 2007-05-27 14:30:01 →
  Size: 6350
  Editor: cosiapat1
  Comment:
+  ← Revision 67 as of 2007-11-27 22:04:45 →
  Size: 8723
  Editor: cosiapat1
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 14:
+ * [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
-Line 24:
+Line 36:
+ * [http://prefuse.org/ Prefuse] - Interactive information visualization library

 * [http://openjgraph.sourceforge.net/ OpenJgraph] - Java graph layout
-Line 28:
+Line 42:
+ * [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++
-Line 36:
+Line 53:
-= 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 MiMs? || || || ||<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 || || || || ||

||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 || || || || || || || || || || ||

Diff for "Network_analysis_links"

Software applications

Programming Libraries

Layouts

Other link directories

Network Visualization

Competitive Landscape (Under Construction)