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

BMC Bioinformatics. 2012;13 Suppl 8(Suppl 8):S3. doi: 10.1186/1471-2105-13-S8-S3. Epub 2012 May 18.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Biochemistry*
  • Cells / metabolism
  • Computer Systems
  • Image Processing, Computer-Assisted
  • Models, Biological*
  • Signal Transduction
  • Software*
  • Systems Biology / instrumentation
  • Systems Biology / methods