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 current visualizer is implemented by Noah Liguori-Bills
(https://noahlb123.github.io/),
a former UConn student, currently PhD student at NCSU.