Features Page is Under Development as of April 18, 2013

Proposed sigViz App Features

1. Visualization of signaling pathways

sigViz will generate structural representations of signaling components and graphic interaction connections directly from data with minimal user input required as in fig 1B–D. Extending our embedded Python Molecular Viewer (http://epmv.scripps.edu) software with threads into to Cytoscape (http://www.cytoscape.org) will provide a sensible development platform that will minimize redundant effort by assembling existing tools where possible. Scripting novel interfaces with our ubiquitous Python API (http://upy.scripps.edu) will make the tools instantly accessible in a variety of hosting software packages including molecular viewers, professional 3D animation applications and web browsers.

2. Pathway animation

Signaling pathways are dynamic by nature and the arrows and other icons (called edges) connecting the molecular nodes in signal pathway diagrams indicate specific interaction types. To clearly show how all these interactions lead to a particular outcome for a variety of audiences, sigViz will allow the edges to be ordered and played in sequence/parallel to animate the pathways as dynamic entities rather than requiring a viewer to mentally connect the interactions– similar to the animated version linked from fig 1D.

3. Pathway interaction

Similar to Cytoscape, but distilled for use with signaling pathways, users can intuitively modify nodes and edges in the modeled cell signaling pathways to reveal or predict consequences, fig 1B–C. We have begun developing an interface based on this sketch, intended to allow a novice to build and run a sigViz cell signaling pathway model with zero Cytoscape experience (they need only install Cytoscape, install sigViz, and run the sigViz App from the Cytoscape menu as instructed.

4. Logic visualization as a thinking tool and an educational tool

Our software will have visual representations that distinguish between different signal state details (rather than the traditional binary on/off) in a clear manner and will animate the temporal control, again, isolating best methods from the massive Cytoscape libraries, fig 1B–C.