Chylek, L. A., Holowka, D. A., Baird, B. A., & Hlavacek, W. S. (2014). AN INTERACTION LIBRARY FOR THE FcεRI SIGNALING NETWORK. Frontiers in Immunology, 5, 1–42. https://doi.org/10.3389/fimmu.2014.00172
Supplementary Files 1-3 are BioNetGen input files with .bngl extensions. They are plain-text files that can be processed by BioNetGen (http://bionetgen.org).
The complete library of rules is given in Supplementary File 1. This file can be simulated with BioNetGen, which uses the built-in network-free simulator (NFsim) to produce simulation results because the full reaction network is too large to enumerate. However, this file is not meant to provide a model but rather a library of rules from which models can be constructed. Simulation instructions that can be passed to NFsim, which can be invoked separately, are included in Supplementary File 4, which is a plain-text file with a .rnf extension.
Supplementary File 2 provides an executable specification of the example model of Fig. 5. This file can be processed by BioNetGen to produce simulation results.
Supplementary File 3 provides an executable specification of the example model of Fig. 7. This file can be processed by BioNetGen to produce simulation results.
A modified form of the File 2 model was used to generate Fig. 6, and a modified form of the File 3 model was used to generate Fig. 8. For both sets of simulations, an input representing a stimulus was used to control the rate of activation of Syk and Fyn. Syk and Fyn were both deactivated through first-order processes. The extra rules and parameters are below. The level of stimulus is set to a number between 0 and 1, which causes generation of active Syk and Fyn.
Parameters: ksynthS 0.5*SimProteinTot # This number will be the steady-state level of active Syk when stimulus is set to 1 kdegS 1 ksynthF 0.5*SimProteinTot # This number will be the steady-state level of active Fyn when stimulus is set to 1 kdegF 1 Rules: # Syk is activated stimulus -> stimulus + Syk(cat) ksynthS # Syk is deactivated Syk(cat) -> zero kdegS # Fyn is actvated stimulus -> stimulus + Fyn(cat) ksynthF # Fyn is deactivated Fyn(cat) -> zero kdegF
A slightly simpler way to implement this using newer BNGL syntax is as follows:
0 <-> Syk(cat) stim*SykTot*kdegS, kdegS 0 <-> Fyn(cat) stim*FynTot*kdegF, kdegF
where SykTot and FynTot are the desired steady state levels of Syk and Fyn respectively and stim is used to determine the fraction of these levels that are achieved.