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* [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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= Competitive Landscape (Under Construction) = ||'''Feature''' ||'''Cytoscape''' ||'''Gen''''''MAPP''' ||'''Pathway Commons''' ||'''Jubilant''' ||'''Ariadne''' ||'''Ingenuity''' ||'''Gene''''''Go''' ||'''pajek''' ||Visant||'''Cell''''''Designer''' || |
= Competitive Landscape (Under Construction) = ||'''Feature''' ||'''Cytoscape''' ||'''Gen''''''MAPP''' ||'''Pathway Commons''' ||'''Jubilant''' ||'''Ariadne''' ||'''Ingenuity''' ||'''Gene''''''Go''' ||'''pajek''' ||Visant ||'''Cell''''''Designer''' || |
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| ||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 || || | |
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||charting|| || || || || || || || || || || ||"Enterprise Configuration"|| || || || || || || || || |||| ||Embedded SQL database|| || || || || || || || || |||| ||relevance networks|| || || || || || || || || || || |
||charting || || || || || || || || || || || ||"Enterprise Configuration" || || || || || || || || || || || ||Embedded SQL database || || || || || || || || || || || ||relevance networks || || || || || || || || || || || |
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
[http://gephi.org/ Gephi] - graph exploration and manipulation software
[http://arena3d.org/index.html Arena3D] - Visualizing biological networks in 3D
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++
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 |
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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 |
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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 |
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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 |
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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 |
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16 |
raw data import |
delimited text, .mrna format |
affy, delimited-text |
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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 |
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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 |
via MiMs? |
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YES |
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YES |
charting |
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"Enterprise Configuration" |
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Embedded SQL database |
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relevance networks |
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