October 23rd, 2011
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
Smith, A.M., Xu, W., Sun, Y., Faeder, J.R., Marai, G.E., RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry, 1st IEEE Symposium on Biological Data Visualization (BioVis 2011), Providence, RI, October 23rd, 2011. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355338/pdf/1471-2105-13-S8-S3.pdf