Graph Visualization Software References

VisANT

VisANT
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General software information
Author
See http://visant.bu.edu/community.htm
Website
http://visant.bu.edu/
Presentation
VisANT is a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways.
Supported
Yes
Specific software information
Graph type
2D or 3D
2D graph, 3D graph
Graph size
More than 1 000 000 nodes
Type
Field of uses
Description
Network Module Enrichment Analysis (NMEA) to detect phenotypic difference between two data sets (e.g. gene expression of disease v.s. normal), GO Term Enrichment Analysis (GOTEA) to find the over-represented GO terms in network modules, multi-scale visualization of bio-networks, Exploratory navigation of KEGG pathways and many more features.
Possible uses
Query/Create interaction networks, Use VisANT to visualize networks in your own web site, batch mode to automate the analyses,
Software characteristics
Handling
Interactivity with the graph
Technical aspects
Software size
Development language
Java
Operating system
Java enabled OS
Main references
Article
Hu, Z., et al., (2009) VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. 2009 37: W115-W121.Hu, Z. Mellor, Snitkin, S. E., & DeLisi, C. (2008). VisANT: an integrative framework for networks in systems biology, Briefings in Bioinformatics, 2008;9:317-325.Hu, Z., et al., (2007) VisANT 3.0: new modules for pathway visualization, editing, prediction and construction, Nucl. Acids Res. 2007 33: W352-W357. PDFHu, Z., et al., (2007) Towards zoomable multidimensional maps of the cell. Nat Biotechnol, 25(5): p. 547-54. PDFHu, Z., Mellor, J., Wu, J. and DeLisi, C. (2005) VisANT: data-integrating visual framework for biological networks and modules, Nucl. Acids Res. 2005 33: W352-W357.Hu,Z., Mellor,J. and DeLisi,C. (2004) Analyzing Networks with VisANT, In Current Protocols in Bioinformatics. John Wiley & Sons, New Jersey, US.Hu, Z., Mellor, J., Wu, J. and DeLisi, C. (2004) VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics, 5, 17.
Website
Applications based on this library (only for libraries)
Cost and license
Cost and license
Free
Download link
http://visant.bu.edu/running2.htm
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