A Sample Application for SBGNViz

This is a sample application for the web based library named SBGNViz developed for visualization of process description maps in SBGN.

Software

SBGNViz and this sample application are distributed under GNU Lesser General Public License.

A deployment of this sample application can be found here. SBGNViz works on every platform that have Javascript support including mobile devices.

Please cite the following when you use SBGNViz.js:

M. Sari, I. Bahceci, U. Dogrusoz, S.O. Sumer, B.A. Aksoy, O. Babur, E. Demir, "SBGNViz: a tool for visualization and complexity management of SBGN process description maps", PLoS ONE, 10(6), e0128985, 2015.

Running a Local Instance

In order to deploy and run a local instance of the tool, please follow the steps below:

• Installation

git clone https://github.com/iVis-at-Bilkent/sbgnviz.js-sample-app.git
cd sbgnviz.js-sample-app
npm install 

• Running the tool

npm run debug-build

Then, open a web browser and navigate to localhost:3000. Please note that the default port is 3000 but you can run this application in another port by setting 'port' environment variable.

Highlights

Below are some sample screenshots from SBGNViz.js sample application, illustrating some of its capabilities. Please click on a figure to see it in full size.

Mapk cascade pathway visualized in SBGNViz.js	Highlighting processes of selected node group
Hiding selected node group	Same graph after applying hiding on selected node group
Showing only selected node group	Same graph after showing only selected node group
Highlighting neighbors of selected node group	Load SBGN-PD diagram from an sbgn-ml file
Loading an sbgnml file from file explorer	SBGN diagram visualization of Glycolysis after loading its sbgnml file
Saving current SBGN process description diagram as an sbgnml file	Saving current SBGN process description diagram as a png file

Credits

Icons made by Freepik, Daniel Bruce, TutsPlus, Robin Kylander, Catalin Fertu, Yannick, Icon Works, Flaticon and licensed with Creative Commons BY 3.0

Thanks to JetBrains for an Open Source License

Team

• Metin Can Siper, Selim Firat Yilmaz, Ugur Dogrusoz, and Alper Karacelik of i-Vis at Bilkent University

Alumni

• Istemi Bahceci, Mecit Sari, Ayhun Tekat, M.Furkan Sahin