Rules_Rail_Road - visualizing rule-based models

About rail-road diagrams

• Syntax and Railroad diagrams ( https://en.wikipedia.org/wiki/Syntax_diagram)
   
• Python and JavaScript libraries for generating railroad diagrams by Tab Atkins Jr. ( https://github.com/tabatkins/railroad-diagrams).

About rule-based modeling

• The original BioNetGen software and scripting language for the description of models was designed in 2004:
  Blinov, M. L., Faeder, J. R., Goldstein, B., & Hlavacek, W. S. (2004). BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics, 20(17), 3289-3291. PMID:15217809
   
• The concept of rule-based modeling as a graph rewriting was introduced in 2006:
  Blinov, M. L., Yang, J., Faeder, J. R., & Hlavacek, W. S. (2006). Graph theory for rule-based modeling of biochemical networks. Transactions on Computational Systems Biology VII (pp. 89-106). Berlin, Heidelberg: Springer Berlin Heidelberg.
   
• The most comprehensive description of rule-based modeling using BioNetGen was published in 2009:
  Faeder, J. R., Blinov, M. L., & Hlavacek, W. S. (2009). Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol. 500:113-67. PMID:19399430
   
• The advanced BioNetGen 2.0 was described in 2016:
  Harris, L. A., Hogg, J. S., Tapia, J. J., Sekar, J. A., Gupta, S., Korsunsky, I., ... & Faeder, J. R. (2016). BioNetGen 2.2: advances in rule-based modeling. Bioinformatics, 32(21), 3366-3368. PMID:27402907
   
• Rule-based modeling was introduced into the VCell modeling and simulation framework in 2016:
  Schaff, J. C., Vasilescu, D., Moraru, I. I., Loew, L. M., & Blinov, M. L. (2016). Rule-based modeling with Virtual Cell. Bioinformatics, 32(18), 2880-2882. PMID:27497444
   
• The compartmental rule-based modeling in VCell was introduced in 2017:
  Blinov, M. L., Schaff, J. C., Vasilescu, D., Moraru, I. I., Bloom, J. E., & Loew, L. M. (2017). Compartmental and spatial rule-based modeling with virtual cell. Biophysical journal, 113(7), 1365-1372. PMID:28978431
   
• The first web visualier for rule-based modeling bnglViz was implemented in 2024:
  Liguori-Bills, N., & Blinov, M. L. (2024). bnglViz: online visualization of rule-based models. Bioinformatics, 40(6), btae351. PMID:38814806
   

Acknowledgement

• The concept of using Rail Road diagrams for describing rule-based models was first discussed in 2022 by Michael Blinov and a mathematician Ellis D. Cooper.
• The first attempt to visualize rule-based modeling was done by UConn undegraduate HRP student Chandrika Dhavala
• The current visualizer is implemented by UConn undegraduate HRP student Reesha Patel (https://github.com/reeshapatel12/).