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

Smith, Adam M ; Xu, Wen ; Sun, Yao ; Faeder, James R ; Marai, G Elisabeta

BMC bioinformatics, 2012, Vol.13 Suppl 8, pp.S3 [Rivista Peer Reviewed]

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  • Titolo:
    RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry
  • Autore: Smith, Adam M ; Xu, Wen ; Sun, Yao ; Faeder, James R ; Marai, G Elisabeta
  • Note di contenuto: 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. 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. 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.
  • Fa parte di: BMC bioinformatics, 2012, Vol.13 Suppl 8, pp.S3
  • Soggetti: Biochemistry ; Models, Biological ; Software
  • Lingua: Inglese
  • Tipo: Articolo
  • Identificativo: E-ISSN: 1471-2105 ; PMID: 22607382 Version:1 ; DOI: 10.1186/1471-2105-13-S8-S3
  • Fonte: MEDLINE/PubMed (U.S. National Library of Medicine)

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