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This article is part of the supplement: Highlights of the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011)

Open Access Research

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

Adam M Smith1*, Wen Xu1, Yao Sun1, James R Faeder2 and G Elisabeta Marai12*

Author affiliations

1 Department of Computer Science, University of Pittsburgh, Pittsburgh, 15260, USA

2 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, USA

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Citation and License

BMC Bioinformatics 2012, 13(Suppl 8):S3  doi:10.1186/1471-2105-13-S8-S3

Published: 18 May 2012

Abstract

Background

Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less error prone, and to improve workflows.

Results

We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. We present the user requirements, visual paradigms, algorithms and design decisions behind RuleBender, with emphasis on visual global/local model exploration and integrated execution of simulations. The support of RBM creation, debugging, and interactive visualization expedites the RBM learning process and reduces model construction time; while built-in model simulation and results with multiple linked views streamline the execution and analysis of newly created models and generated networks.

Conclusion

RuleBender has been adopted as both an educational and a research tool and is available as a free open source tool at http://www.rulebender.org webcite. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community.