#biographer

is a biological network layout and visualization tool which has been developed at the Theoretical Biophysics Group in Berlin as part of the Google Summer of Code 2011.

It consists of a layout algorithm C/C++ library (_biographer-layout_) which creates an graph layout optimized for biological networks, especially for bi-partite reaction graphs and a Javascript web component (_biographer-visualization_) for interactive in-browser visulalization of those networks. A server component (_biographer-server_) puts all sub projects together and provides network import from various sources and subsequent visualization.

The project wiki gives detailed descriptions on the sub projects and contains the build instructions.

The current version of the editor provides import and export functions as well as editing and visualization options. If the editor is not available through biographer.biologie.hu-berlin.de alternatively you can reach it under http://semanticsbml.org/biographer

NetworkExplorer is a project demo which visualizes the Network data from the Reactome and PID databases. The network can be explored by clicking through the different pathways.

biographer is based on jSBGN, a lightweight JSON network exchange format which lies between biological model description languages like SBML and full glyph describing languages like SBGN-ML or SVG. The jSBGN definition can be found here. biographer can handle SBML and SBGN-ML through the jSBGN.js library

If you have questions about the project you can contact us via the public mailing list biographer@googlegroups.com. If you would like to contact the developers directly please use biographer-dev@googlegroups.com.

• Thomas Handorf
• Marvin Schulz
• Falko Krause
• Matthias Bock
• Ben Ripkens
• Acer Wei Jing
• Max Flöttmann
• Till Scharp
• Taye Adeyemi
• Lian Duan
• Chaitanya Talnikar