NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto) is a software and analysis tool for visualizing and analyzing protein-protein interaction networks. The tool enables academics to interpret integrated cancer profiles and create dynamic models. NAViGaTOR can query Online Predicted Human Interaction Database (OPHID) and Interologous Interaction Database (I2D), online interaction databases, and display 2- or 3-dimensional networks on multiple hardware platforms to improve scalability and performance. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as Gene Ontology (GO) and the Proteomics Standards Initiative (PSI). NAViGaTOR combines a visualization system implemented in OpenGL with a graphical user interface and analytical algorithms implemented in Java. In protein-protein interaction networks, nodes represent proteins and edges between nodes represent physical interactions between the proteins. NAViGaTOR allows nodes and edges to be colour-coded according to GO terms and according to experimentally-gathered information regarding the expression of proteins and the correlations between proteins. These visualizations allow for insights into the proteins that play key roles in various diseases such as cancer. NAViGaTOR is under active development by Dr. Igor Jurisica and his laboratory of the Ontario Cancer Institute. Dr. Jurisica is the Canada Research Chair in Integrative Computational Biology.

NAViGaTOR is freely-downloadable to academic users from the downloads section of the website available at: http://ophid.utoronto.ca/navigator/downloads.html. The application can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. Users can load networks from a tab-delimited file (e.g. NAViGaTOR XML, BioPAX or PSI formats), or can be generated dynamically by executing a visual query to the Interologous Interaction Database (I2D), an online database of known, HTP, and predicted protein-protein interactions for human, rat, mouse, fly, worm, and yeast or cPath. The website also provides tutorials for users in HTML or Flash format to help with navigating the software.