RuleBender: Integrated visualization for biochemical rule-based modeling

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TitleRuleBender: Integrated visualization for biochemical rule-based modeling
Publication TypeConference Paper
Year of Publication2011
AuthorsSmith, AM, Xu, W, Sun, Y, Faeder, JR, G. Marai, E
Conference Name2011 IEEE Symposium on Biological Data Visualization (BioVis)2011 IEEE Symposium on Biological Data Visualization (BioVis).
PublisherIEEE
Conference LocationProvidence, RI, USA
ISBN Number978-1-4673-0003-2
Accession Number12408402
KeywordsAnalytical models, Biological system modeling, Computational modeling, Data visualization, Mathematical model, Proteins, Visualization
Abstract

We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intra-cellular biochemistry. 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 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. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community.

URLhttp://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6094054
DOI10.1109/BioVis.2011.6094054
Refereed DesignationUnknown