Gillespie Algorithm Simulation

The Gillespie algorithm We now return to explain the Gillespie algorithm for simulating multiple chemical reactions in a well-mixed environment.

Definition The Gillespie Algorithm, also known as the Stochastic Simulation Algorithm SSA, is a computer-oriented procedure for simulating the changes in the molecular populations of chemical species in a chemically reacting system. The algorithm requires the reactant molecules, typically solute molecules in a sea of many much smaller solvent molecules, to be dilute and well-mixed throughout

One prominent computational algorithm for understanding stochasticity in gene expression is the Gillespie algorithm also known as the Stochastic Simulation Algorithm 11, 12. The Gillespie algorithm is an extremely efficient computational technique used to simulate the time evolution of a system in which events occur randomly and discretely

The Gillespie algorithm The transition probabilities are also called propensities in the context of stochastic simulation. The propensity for a given transition, say indexed i, is denoted as ai.

Gillespie Algorithm In this blog post we will look at the grand-daddy of stochastic simulation methods the Gillespie Algorithm otherwise known as the stochastic simulation algorith SSA. If you have ever done any form of stochastic simulation you will owe a great deal of gratitude to the Gillespie algorithm which likely inspired the techniques you used. Apr 14, 2020 Lewis Cole 2020

The Gillespie algorithm, also called a stochastic simulation algorithm SSA, is a way to sample the story behind a master equation, as will become clear momentarily as we work through the algorithm and introduce some terminology. The transition probabilities are also called propensities in the context of stochastic simulation.

Exact simulation of birth-death processes via the Gillespie algorithm ICTP Workshop on Mathematical Models of Climate Variability, Environmental Change and Infectious Diseases Aaron A. King 8-19 May 2017

Gillespie simulation of the chemical master equation As an alternative method to sample the joint mRNA protein distribution Pm, p P m, p we can use the Gillespie algorithm. This is a great alternative since the algorithm is widely used in many fields and therefore its intuitive implementation is familiar to a broad audience.

The Gillespie algorithm or SSA is a discrete-event simulation algorithm that produces single realizations of the stochastic process that are in exact statistical agreement with the master equation. This submission includes simple implementations of the two original versions of the SSA Direct and First-Reaction Method.

Gillespie algorithm In probability theory, the Gillespie algorithm or the Doob-Gillespie algorithm or stochastic simulation algorithm, the SSA generates a statistically correct trajectory possible solution of a stochastic equation system for which the reaction rates are known.