Catalyst: Fast and flexible modeling of reaction networks
Fig 2
Catalyst models can be simulated using both deterministic and stochastic interpretations.
(a) The Brusselator network contains two species (X and Y) and two parameters (A and B, in practical implementation these are species present in excess, but they can in practice be considered parameters) [39, 40]. Here, we show the four reactions of the Brusselator CRN, and its implementation using the Catalyst DSL. (b-d) Simulations of models for the Brusselator at the three physical scales supported by Catalyst (RRE, CLE, SSA). Post-processing has been carried out on the plots to improve their visualization in this article’s format. (b) While B > 1 + A2, the deterministic model exhibits a limit cycle. This is confirmed using ODE RRE simulations. (c) The model can also be simulated using the stochastic CLE interpretation. (d) Finally, the discrete, stochastic, jump process interpretation is simulated via Gillespie’s direct method. The system displays a limit cycle even though B < 1 + A2, confirming the well known phenomenon of noise induced oscillations [41].