Department of Computer Science, University of Pittsburgh, PA 15260, USA.
BMC Bioinformatics. 2012;13 Suppl 8(Suppl 8):S3. doi: 10.1186/1471-2105-13-S8-S3. Epub 2012 May 18.
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.
基于规则的建模（RBM）是一种强大且越来越流行的细胞信号网络建模方法。然而，需要新颖的可视化工具才能使广泛的用户能够使用 RBM，减少模型规范中的错误，并改进工作流程。
我们引入了 RuleBender，这是一种用于基于规则的细胞内生物化学的集成可视化、建模和模拟的新型可视化系统。我们介绍了 RuleBender 的用户需求、视觉范例、算法和设计决策，重点介绍了可视化全局/局部模型探索和集成执行模拟。RBM 创建、调试和交互式可视化的支持加快了 RBM 的学习过程并减少了模型构建时间；而内置的模型模拟和具有多个链接视图的结果简化了新创建模型和生成网络的执行和分析。
RuleBender 已被用作教育和研究工具，并可在 http://www.rulebender.org 上免费获得开源工具。一个包括与专家用户密切互动的开发周期使 RuleBender 能够更好地满足系统生物学社区的需求。
