NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Summary: NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture. Availability: NAViGaTOR is freely available to the research community from http://ophid.utoronto.ca/navigator/. Installers and documentation are provided for 32- and 64-bit Windows, Mac, Linux and Unix. Contact: juris@ai.utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.

[1]  M. Tyers,et al.  The GRID: The General Repository for Interaction Datasets , 2003, Genome Biology.

[2]  Igor Jurisica,et al.  Online Predicted Human Interaction Database , 2005, Bioinform..

[3]  George Chin,et al.  BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment , 2008, BMC Bioinformatics.

[4]  Dipanwita Roy Chowdhury,et al.  Human protein reference database as a discovery resource for proteomics , 2004, Nucleic Acids Res..

[5]  Zhenjun Hu,et al.  VisANT: an online visualization and analysis tool for biological interaction data , 2004, BMC Bioinformatics.

[6]  Kyungsook Han,et al.  Complexity management in visualizing protein interaction networks , 2003, ISMB.

[7]  S. L. Wong,et al.  Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.

[8]  Matthew Suderman,et al.  Tools for visually exploring biological networks , 2007, Bioinform..

[9]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[10]  Stephen G. Kobourov,et al.  Journal of Graph Algorithms and Applications Grip: Graph Drawing with Intelligent Placement , 2022 .

[11]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[12]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[13]  Edward M. Reingold,et al.  Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..

[14]  M. Tyers,et al.  Osprey: a network visualization system , 2003, Genome Biology.

[15]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[16]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[17]  Robert Hoffmann,et al.  HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms , 2005, BMC Bioinformatics.

[18]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[19]  David L. Robertson,et al.  JNets: Exploring networks by integrating annotation , 2009, BMC Bioinformatics.

[20]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[21]  Natasa Przulj,et al.  High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells , 2005, Science.

[22]  Jussi Paananen,et al.  FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data , 2009, BMC Systems Biology.