BioSimulator.jl: Stochastic simulation in Julia.

ABSTRACT:

Background and objectives

Biological systems with intertwined feedback loops pose a challenge to mathematical modeling efforts. Moreover, rare events, such as mutation and extinction, complicate system dynamics. Stochastic simulation algorithms are useful in generating time-evolution trajectories for these systems because they can adequately capture the influence of random fluctuations and quantify rare events. We present a simple and flexible package, BioSimulator.jl, for implementing the Gillespie algorithm, τ-leaping, and related stochastic simulation algorithms. The objective of this work is to provide scientists across domains with fast, user-friendly simulation tools.

Methods

We used the high-performance programming language Julia because of its emphasis on scientific

SUBMITTER: Landeros A 

PROVIDER: S-EPMC6388686 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature