To advance currently used web-based signaling network visualization techniques, AJAX Viewer of Interactive Signaling Networks (AVIS) provides several important enhancements not currently available in other techniques/systems. It allows cross platform visualization of signaling networks with integrated zoom and pan functionality without requiring installation of a third party plug-in. AVIS is implemented using AJAX (Adams, 2005
; Garrett, 2005
Screenshot of AVIS as running as a Google Gadget embedded in a webpage with its default settings.
The layout of the nodes in maps is accomplished by the fileloader module. This provides developers with an easy way to add to AVIS additional layout algorithms. The included fileloaders that we implemented can be configured to use all of currently available Graphviz layout algorithms: dot, neato, fdp, circo and twopi. Alternatively, file formats, such as the Pajek.net file format (Batageli and Mryar, 2003) and a native.avis file format we developed (described in the manual) can include the layout in the input text file. As such, other layout programs can be used before importing into AVIS. Alternatively, a simple Perl wrapper can be added to automatically import other layout algorithms.
The graph rendering is accomplished by one of the two included graph drawing modules or by a user-defined graph drawing module. The default rendering functions generate a layout.dot file, calling Graphviz to do the actual rendering. In AVIS we implemented an alternative option: AVISgraphDraw. AVISgraphDraw uses PerlMagick (ImageMagic) image drawing API to draw the network map images. Both of these options are fairly simple graph rendering tools, but can draw a wide variety of networks as long as they can be described in terms of properties such as positions, shapes, size, colors of nodes, and placement and paths of edges. If more sophisticated graph rendering tools with other features are required, it is simple to add a Perl wrapper for such tools. The process of developing such wrappers is described in the user manual.
AVIS supports several standard graph representation formats such as Pajek.net (Batageli and Mryar, 2003) and Systems Biology Markup Language (SBML) (Deckard et al., 2006
; Kitano et al., 2005
) as well as a simple structured text file format we developed called .sig (Ma’ayan et al., 2005
). It also supports a more flexible native.avis format which allows editing of any graph features, giving users more control over the placement of nodes, colors of nodes and arrows, shapes of nodes and types of arrows as well as more control on setting up hyperlinks. AVIS was implemented for visualization of PathwayGenerator, a tool that displays over 4000 automatically generated mammalian cell signaling maps created from a large-scale literature-based neuronal cell signaling network we developed (Ma’ayan et al., 2005
); AVIS was also implemented for visualization of NodeNeighborhood: a tool to visualize first and second interacting neighbors of mammalian proteins based on data from the IntAct database (Kerrien et al., 2007
) as well as two yeast-2-hybrid studies of mammalian protein interactions; and AVIS was implemented in Genes2Networks, a tool that can be used to create subnetworks from lists of genes and proteins by using 10 background mammalian protein interaction networks to ‘connect’ seed lists of gene symbols.
Other visualization programs are compatible with standards such as BioPAX, and PSI-MI (Stromback and Lambrix, 2005
). AVIS can be adapted and upgraded to support any of these formats with simple Perl wrapped plug-ins. We hope that interested developers would find this tool easy to leverage for visualization of their system of interest.