RuleBender: Integrated visualization for biochemical rule-based modeling

Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai
2011 2011 IEEE Symposium on Biological Data Visualization (BioVis).  
Fig. 1 . The RuleBender interface. Shown are the Model Editor pane including console for text output (left) and the Visualization Viewer pane (right). The Visualization Viewer shows two complementary visual encodings corresponding to the text model in the Editor: the interactive contact map (top), and part of the influence graph for this model (bottom). RuleBender's main features include syntax checking, syntax highlighting, visual global model exploration with linked views, integrated
more » ... integrated execution, support for multiple simulation modules, simulation journaling, interactive plotting including comparison of multiple datasets, and parameter scanning. Abstract-We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rulebased intracellular 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 particular 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 analysis 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.
doi:10.1109/biovis.2011.6094054 dblp:conf/biovis/SmithXSFM11 fatcat:gb5ac3r7ibamddyvjvxbgrutlu