BioSimulator.jl: Stochastic simulation in Julia. (December 2018)

• Record Type: Journal Article
• Authors: Landeros, Alfonso; Stutz, Timothy; Keys, Kevin L.; Alekseyenko, Alexander; Sinsheimer, Janet S.; Lange, Kenneth; Sehl, Mary E.
• Is Part Of: Computer methods and programs in biomedicine. Volume 167(2018)
• Page Start: 23
• Page End: 35
• Publication Date: 2018-12
• Subjects: Stochastic simulation -- Gillespie algorithm -- τ-leaping -- Systems biology -- Julia language; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2018.09.009
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: This work highlights BioSimulator.jl, an open-source master equation simulation engine implemented in the Julia language. We highlight the comparative strengths of the exact and approximate stochastic simulation algorithms provided by our software. Stochastic simulation finds applications across disciplines, including ecology, chemistry, and genetics. We illustrate BioSimulator.jl's workflow and utility with examples. Our benchmarks favor a Julia implementation: BioSimulator.jl provides code readability and ease-of-use without sacrificing performance. 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 languageJulia because of its emphasis on scientific computing. Our software package implements a suite of stochastic simulation algorithms based on Markov chain theory. We provide the ability to (a) diagram Petri Nets describing interactions, (b) plot average trajectories and attached standard deviations of each participating species over time, and (c) generate frequency distributions of each species at a specified time. Results :BioSimulator.jl 's interface allows users to build models programmatically withinJulia . A model is then passed to thesimulate routine to generate simulation data. The built-in tools allow one to visualize results and compute summary statistics. Our examples highlight the broad applicability of our software to systems of varying complexity from ecology, systems biology, chemistry, and genetics. Conclusion : The user-friendly nature ofBioSimulator.jl encourages the use of stochastic simulation, minimizes tedious programming efforts, and reduces errors during model specification.