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

Created on October 23, 2011

2011   ·   paper   ·   papers

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

Smith, A.M., Xu, W., Sun, Y., Faeder, J.R., Marai, G.E.

image Contact Map with molecule compartment hierarchy (extracellular, cytoplasmic, nucleus etc).

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. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community