BLeaping

The BLeaping solver implements an explicit tau leaping method with a fixed step size 1. Here, the fixed step size is assumed to be small enough such that propensity function values do not change dramatically between time steps.

Skipping tau selection and thus never reverting back to Gillespie (SSA) may speed up the simulation time. However, accuracy is expected to be low, and it is possible to reach negative population. When the latter phenomenon occurs, the BLeaping solver sets the corresponding population to zero and displays a warning message recommending that you reduce the time step size.

Parameter

Data type

Default

Description

solver

string

NA

B, BLeap, and BLeaping are all valid names to run this solver.

Tau

float

0.1

The size of the fixed time step used throughout the simulation.

Example

{
    "duration": 5,
    "runs": 5000,
    "solver": "B",
    "samples": 50,
    "prng_seed": 123,
    "b-leaping": {
        "Tau"  : 0.01
    }
} 
1

Gillespie, Daniel T. “Approximate accelerated stochastic simulation of chemically reacting systems.” Journal Of Chemical Physics 115 4 (2001)