BioSimulator.jl: Stochastic simulation in Julia.

Computer Methods and Programs in Biomedicine(2018)

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摘要
•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.
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关键词
Stochastic simulation,Gillespie algorithm,τ-leaping,Systems biology,Julia language
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