Gillespie.jl: Stochastic Simulation Algorithm in Julia
Recommend Documents
Gillespie.jl (Frost 2016) is a Julia package for stochastic simulation using Gillespie's di- rect method (sometimes called the Doob-Gillespie algorithm) (Doob ...
for each one of the M reaction channels, is sampled from ... Tian and Burrage3 and Chatterjee .... -leaping assumption that the propensities aj x 1j M re-.
Artificial chemistries (AC) are useful tools and a simple shortcut for the ... should be large and have a huge number of
Jan 19, 2011 - An Efficient Stochastic Simulation Algorithm for Bayesian Unit Root Testing in Stochastic. Volatility Models. Yong Li · Zhongxin Ni · Jie Zhang.
Sep 5, 2014 - C. Lester,a) C.A. Yates, M.B. Giles, and R.E. Baker. Mathematical Institute, Andrew Wiles Building, Radcliffe Observatory Quarter,. Woodstock ...
Feb 7, 2011 - Monte Carlo technique, so-called stochastic simulation algorithm (SSA). The SSAs lend themselves accurately well to stochasticity in GRNs ...
The weighted stochastic simulation algorithm wSSA recently introduced by Kuwahara and Mura. J. Chem. Phys. 129, 165101 2008 is an innovative variation on ...
Nov 9, 2012 - The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are ... simulation of complex sets of interconnected chemical reaction.
The three-dimensional high-order simulation algorithm HOSIM is developed to simulate .... The stochastic simulation based on high-order spatial cumulants for.
An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm SSA, is proposed. The present ...
this paper, a stochastic leap-frog algorithm for the numeri- cal integration of Langevin stochastic differential equations with multiplicative noise is proposed and ...
Jan 3, 2014 - Citation: Sun Y, Chen L, Xu R, Kong R (2014) An Image Encryption Algorithm Utilizing Julia Sets and Hilbert Curves. PLoS ONE 9(1): e84655.
Aug 1, 2017 - Quantum Optics Simulation using. QO-Julia by. Fabian Mitterwallner supervisor. Univ. Prof. Dr. Helmut Ritsch. Institute for Theoretical Physics.
Aug 1, 2017 - and is modeled after the Quantum Toolbox in Python(QuTip). The following will explain how a problem can be defined using QuantumOptics.jl.
9. 3 Sensitivity Analysis. 11. 3.1 Example: Michaelis-Menten . ..... Notebook. This launches a Jupyter Notebook, with a template for analyzing the data.
This paper describes the M-Xplore extension of the Radioss software. ... One of the first applications of M-Xplore was a statistical investigation for a complete car.
modifications to the NORTA procedure can help it achieve close approximations to the desired ...... In Chapter 4 we study certain modifications to the initialization phase of NORTA that ...... conjecture that this should be a relatively straightforwa
Stochastic Simulation in Surface Reconstruction and. Application to 3D Mapping. Jeff Leal, Steve Scheding and. â . Gamini Dissanayake. Australian Centre for ...
Xu'nan Yang, Lin Zhao, Lili Song, Genshen Fang and Yaojun Ge ... and the cross-correlation between the moving distance and the moving turning angle.
Abstract. In this paper a population balance based mathematical model is presented for describing suspension polymerization of vinyl chloride. The properties of ...
Advances in Stochastic. Simulation Methods. N. Balakrishnan. V.B. Melas. S. Ermakov. Editors. Birkhäuser. Boston ⢠Basel ⢠Berlin ...
Feb 3, 2014 - Interest in stochastic simulations of chemical systems is growing. ... simulation algorithm, the nested stochastic simulation algorithm and the ...
want my therapist to break into tears and say, "That's horrible. That's terrible," and we're both .... internet. Julia:
Jesse is a journalist, formerly a Senior Editor for. New York Magazine's website ...... strikes me as kind of unethical
Gillespie.jl: Stochastic Simulation Algorithm in Julia
ACS Publications: 2340â61. doi:10.1021/j100540a008. Pineda-Krch, Mario. 2008. âGillespieSSA: Stochastic Simulation Algorithm in R.â Jour- nal of Statistical ...
Gillespie.jl: Stochastic Simulation Algorithm in Julia Simon DW Frost1 DOI: 10.21105/joss.00042
1 University of Cambridge
Software • Review • Repository • Archive Licence Authors of JOSS papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (CC-BY).
Summary Gillespie.jl (Frost 2016) is a Julia package for stochastic simulation using Gillespie’s direct method (sometimes called the Doob-Gillespie algorithm) (Doob 1945; Gillespie 1977), an approach widely used in many fields, including systems biology and epidemiology. It borrows the basic interface (although none of the code) from the R library GillespieSSA by Mario Pineda-Krch (Pineda-Krch 2008), although Gillespie.jl only implements the standard exact method at present, whereas GillespieSSA also includes other methods, such as tau-leaping, etc.. Gillespie.jl is intended to offer performance on par with hand-coded C code, while maintaining a simple but flexible interface.
References Doob, Joseph L. 1945. “Markoff Chains–Denumerable Case.” Transactions of the American Mathematical Society 58 (3). JSTOR: 455–73. doi:10.2307/1990339. Frost, Simon D.W. 2016. “Gillespie.jl: Stochastic Simulation in Julia.” https://github. com/sdwfrost/Gillespie.jl. Gillespie, Daniel T. 1977. “Exact Stochastic Simulation of Coupled Chemical Reactions.” The Journal of Physical Chemistry 81 (25). ACS Publications: 2340–61. doi:10.1021/j100540a008. Pineda-Krch, Mario. 2008. “GillespieSSA: Stochastic Simulation Algorithm in R.” Journal of Statistical Software 25: 12. doi:10.18637/jss.v025.i12.
Frost, (2016). Gillespie.jl: Stochastic Simulation Algorithm in Julia. Journal of Open Source Software, 1(3), 42, doi:10.21105/joss.00042
