title: RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Computer Science, University of Pittsburgh, PA 15260, USA. ams292@cs.pitt.edu
authors.forename: Adam M
authors.initials: AM
authors.lastname: Smith
authors.forename: Wen
authors.initials: W
authors.lastname: Xu
authors.forename: Yao
authors.initials: Y
authors.lastname: Sun
authors.forename: James R
authors.initials: JR
authors.lastname: Faeder
authors.forename: G Elisabeta
authors.initials: GE
authors.lastname: Marai
mesh_terms: D000465:Algorithms; D001671:Biochemistry; D002477:Cells / Q000378:metabolism; D003199:Computer Systems; D007091:Image Processing, Computer-Assisted; D008954:Models, Biological; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000295:instrumentation / Q000379:methods