CircadianOsciallator.bngl
: A more complex model of an activator/repressor system that has a single steady state when simulated with ODE's but can exhibit stable osciallations when simulated with SSA. Demonstrates coupling of binding and synthesis.
Repressilator.bngl
: Three-gene model of synthetic circuit that demonstrates cooperative binding and coupled binding and gene regulation. Also demonstrates use of pla simulation method.