RuleBender: A visual interface for rule-based modeling. 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. Conclusion: 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.
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References in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
- Eshan D. Mitra, Ryan Suderman, Joshua Colvin, Alexander Ionkov, Andrew Hu, Herbert M. Sauro, Richard G. Posner, William S. Hlavacek: PyBioNetFit and the Biological Property Specification Language (2019) arXiv
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- Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno: Labelled port graph -- a formal structure for models and computations (2018)
- Mohammed, Abdulmelik; Czeizler, Elena; Czeizler, Eugen: Computational modelling of the kinetic tile assembly model using a rule-based approach (2017)
- Brim, L.; Nižnan, J.; Šafránek, D.: Compact representation of photosynthesis dynamics by rule-based models (2015)
- Xu, Wen; Smith, Adam M.; Faeder, James R.; Marai, G. Elisabeta: Rulebender: a visual interface for rule-based modeling (2011) ioport