GillespieFirstReaction

The Gillespie First Reaction solver implements the First Reaction Method (FRM) version of the Gillespie algorithm 1. The other version, the Direct Method (DM), is implemented in Gillespie (SSA). While the two methods are theoretically equivalent, they differ in implementation. FRM generates a potential reaction time for every reaction and chooses the reaction corresponding to the earliest reaction time, thus first reaction. In DM implementation, the next reaction time is generated first. Then a reaction is chosen after considering the likelihood of each reaction firing at the computed time.

Parameter

Data type

Description

solver

string

First, FirstReaction, and GillespieFirstReaction are all valid names to run this solver.

Example

{
    "duration": 100,
    "runs": 10000,
    "solver": "First",
    "prng_seed": 10,
    "samples": 120,
    "output": {
        "prefix": "FirstReaction",
        "writecsv": true,
        "compress": false,
        "writeMatFile": false,
        "writeSampleTimes": false
    }
}
1

Gillespie, Daniel T. “Exact stochastic simulation of coupled chemical reactions.” The Journal of Physical Chemistry 81.25 (1977): 2340-361.