Chylek, Lily A., Leonard A. Harris, James R. Faeder, and William S. Hlavacek (2015) “Modeling for (Physical) Biologists: An Introduction to the Rule-Based Approach.” Physical Biology 12, 45007. doi:10.1088/1478-3975/12/4/045007.
- PB2015-SupplementaryfileS1 - IgE receptor signaling
- PB2015-SupplementaryfileS2 - Ligand-receptor binding with diffusion effects
- PB2015-SupplementaryfileS3 - Receptor signaling with a non-trivial basal steady state
- PB2015-SupplementaryfileS4 - Genetic toggle switch
- PB2015-SupplementaryfileS5 - Stochastic gene expression
- PB2015-SupplementaryfileS6 - Model reduced using "fragmentation"
- PB2015-SupplementaryfileS7 - Compartmental (cBNGL) model
- PB2015-SupplementaryfileS8 - Coupled ligand folding and binding using eBNGL ("energy" BioNetGen language)