Abstract

Motivation: The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner.Results: We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats.Availability: The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-indepenent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL.Contact: edda.klipp@biologie.hu-berlin.de or handorf@physik.hu-berlin.de

Highlights

  • The web resource Pathguide (Bader et al, 2006) currently lists 35 databases for ‘Pathway Diagrams’ of biochemical reaction networks, each using different means of visualization and containing at least a two digit number of network graphs

  • Cellular networks in three different languages: Activity Flow diagrams, depicting the flow of information through a network, Entity Relationship diagrams, showing possible interactions of network components, and Process Descriptions (PD), highlighting the temporal order of such interactions, all of which are fully supported by biographer

  • It includes a web service for rendering Systems Biology Graphical Notation (SBGN) and a core library based on HTML5 that can be integrated into other tools and web resources

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Summary

INTRODUCTION

The web resource Pathguide (Bader et al, 2006) currently lists 35 databases for ‘Pathway Diagrams’ of biochemical reaction networks, each using different means of visualization and containing at least a two digit number of network graphs. Web-based visualization tools do not provide ready to use libraries (e.g. Reactome, Joshi-Tope et al, 2005) and/or do not adhere to representation standards (e.g. KEGG, Ogata et al, 1999). Such libraries would be of great help in the development of novel tools supporting SBGN-compliant visualizations. The biographer project is trying to address these needs by providing an open source web-based SBGN renderer and editor. It includes a web service for rendering SBGN and a core library based on HTML5 that can be integrated into other tools and web resources.

SIMPLE USE CASE
USE OF BIOGRAPHER IN OTHER TOOLS
CONCLUSION

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