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Internet Mathematics Volume 7, 2011 - Issue 4: Biological Networks
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Original Articles

NAViGaTOR: Large Scalable and Interactive Navigation and Analysis of Large Graphs

Amira Djebbari Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
,
Muhammad Ali Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
,
David Otasek Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
,
Max Kotlyar Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
,
Kristen Fortney Department of Medical Biophysics, University of Toronto, the Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
,
Serene Wong Department of Computer Science, York University, the Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
,
Anthony Hrvojic Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
&
Igor Jurisica Ontario Cancer Institute, Princess Margaret Hospital/UHN, and the Campbell Family Institute for Cancer Research, IBM Life Sciences Discovery Centre, TMDT Room 9-305, 101 College Street, Toronto, ON, M5G 1L7, Canada
 show all
Pages 314-347 | Received 18 Jan 2011, Accepted 14 Jun 2011, Published online: 30 Nov 2011
 
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Abstract

Network visualization tools offer features enabling a variety of analyses to satisfy diverse requirements. Considering complexity and diversity of data and tasks, there is no single best layout, no single best file format or visualization tool: one size does not fit all. One way to cope with these dynamics is to support multiple scenarios and workflows. NAViGaTOR (Network Analysis, Visualization & Graphing TORonto) offers a complete system to manage diverse workflows from one application. It allows users to manipulate large graphs interactively using an innovative graphical user interface (GUI) and through fast layout algorithms with a small memory footprint. NAViGaTOR facilitates integrative network analysis by supporting not only visualization but also visual data mining.

Acknowledgments

We thank Periklis Andritsos, Wing Xie, and Fiona Broackes-Carter for useful discussion. This research was supported in part by grants from the Natural Sciences and Engineering Research Council (NSERC# 104105), the Canadian Institute for Health Research (CIHR BIO-99745), the Canada Foundation for Innovation (CFI #12301 and #203383), the Ontario Research Fund (GL2-01-030 and RE-03-020), and the Canada Research Chair Program to IJ. This research was funded in part by the Ontario Ministry of Health and Long Term Care (MOHLTC). The views expressed do not necessarily reflect those of the MOHLTC.

Notes

1Available online at http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd (accessed 17-December-2010).

2 Caenorhabditis elegans events in the BioPAX level 2 format. Available online at http://www.reactome.org/download (accessed 4-January-2011).

3Available from Saxonica Limited. “SAXON: The XSLT and XQuery Processor,” http://saxon.sourceforge.net (accessed 17-December-2010) .

4Available online at http://www.imexconsortium.org/ (accessed 17-December-2010).

6Available online at http://ophid.utoronto.ca/navigator/ .

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