TableOfContents

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

• 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)