rebop

rebop is a fast stochastic simulator for well-mixed chemical reaction networks.

It is written in Rust, a modern, safe, and fast language. But it is available as any Python package, through PyPI, so it can be easily installed with pip install rebop.

Stochastic models can then be implemented with a simple API, for example for the classic SIR model:

import rebop

sir = rebob.Gillespie()
# A susceptible individual can be infected by an infected one
#     S + I → I + I     at rate 1e-4
sir.add_reaction(1e-4, ["S", "I"], ["I", "I"])
# An infected individual can recover and become resistant
#         I → R         at rate 0.01
sir.add_reaction(0.01, ["I"], ["R"])

# Run the simulation
ds = sir.run({"S": 999, "I": 1}, tmax=250, nb_steps=250)

The output is an xr.Dataset object which can be plotted:

It can also be used to model more complex systems, with non law of mass action rates:

import rebop

mm = rebop.Gillespie()
# Enzymatic reaction with a Michaelis-Menten rate
#         A → P         at rate V * A / (Km + A)
mm.add_reaction("V * A / (Km + A)", ["A"], ["P"])

params = {"V": 1, "Km": 20}

ds = mm.run({"A": 100}, tmax=250, nb_steps=100, params=params)