Table 1 Comparing codon-based models
| Â | Petri net | TASEP-based (PBN inc.) | ODE |
|---|---|---|---|
Assumption | Deterministic waiting times | Stochastic rate law | Biochemical reaction rates |
Exclusion enforced | Yes | Yes | No |
Update rule | Parallel | Random-sequential or parallel | N.A. |
Solution methods | Analytical, simulations | Analytical, simulations, or numericallyexact (PBN) | Analytical, simulations, bifurcation analysis |
Added complexity | Partly allowed | Allowed | Allowed |