## page was renamed from Network analysis libraries in other programming languages
<<TableOfContents>>

= Software applications =
 * [[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
= 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 =
 * http://ihome.cuhk.edu.hk/~b400559/arraysoft_pathway.html
 * http://bioinformatics.ubc.ca/resources/links_directory/?subcategory_id=82
 * http://www.biochemweb.org/systems.shtml
 * http://www.pathguide.org
= Network Visualization =
 * http://www.visualcomplexity.com/vc/index.cfm
 * http://www.aisee.com/
= 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 || || || || || || || || || || ||