SBGNViz.as: a viewer for pathway models in SBGN Process Description Notation

SBGNViz.as is a web application based on Cytoscape Web to visualize the pathway models represented by SBGN Process Description Notation. SBGNViz.as accepts the pathway models represented in SBGN-ML format.

SBGNViz.as was built by extending the web based data visualization tool CytoscapeWeb to support the SBGN Process Description Notation. SBGNViz.as was developed using Adobe Flash Builder and
[Flex]http://www.adobe.com/products/flex.html technologies.

Software

A sample application using SBGNViz.as can be found here.

SBGNViz.as is distributed under GNU Lesser General Public License. Instructions for obtaining a working copy of the project can be found in README.txt and README_SBGNViz.txt files. SBGNViz.as works on every environment supporting Adobe Flash.

Highlights

Below are some sample screenshots from SBGNViz.as, illustrating some of its capabilities. Please click on a figure to see it in full size. A User's Guide can be found here, documenting all features of the tool.

Glycolysis pathway visualized in SBGNViz.as	Parameters to configure automatic layout
Sample pathway before automatic layout is applied	Sample pathway after automatic layout is applied
Highlighting all processes a selected node is involved in	Inspecting detailed properties of a macromolecule
Saving current process description diagram as PDF	Loading a process description diagram from an SBGN-ML file

Team

• Istemi Bahceci, Ugur Dogrusoz, Mecit Sari, i-Vis at Bilkent University
• S.Onur Sumer, cBio at MSKCC