Stochastic Michaelis Menten model

class pints.toy.stochastic.MichaelisMentenModel(initial_molecule_count)

Simulates the Michaelis Menten Dynamics using Gillespie.

This system of reaction involves 4 chemical species with inital counts initial_molecule_count, and reactions:

• X1+X2 -> X3 with rate k1

• X3 -> X1+X2 with rate k2

• X3 -> X2+X4 with rate k3

Parameters:

initial_molecule_count (Array of size 3 of integers) – Sets the initial molecule count.

References

[1]

https://en.wikipedia.org/wiki/Michaelis-Menten_kinetics

interpolate_mol_counts(time, mol_count, output_times)

Takes raw times and inputs and mol counts and outputs interpolated values at output_times

n_outputs()

Returns the number of outputs this model has. The default is 1.

n_parameters()

See pints.ForwardModel.n_parameters().

simulate(parameters, times)

See pints.ForwardModel.simulate().

simulate_raw(rates, max_time)

Returns raw times, mol counts when reactions occur.

suggested_parameters()

Returns an NumPy array of the parameter values that are representative of the model.

For example, these parameters might reproduce a particular result that the model is famous for.

suggested_times()

Returns an NumPy array of time points that is representative of the model