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10.21105.joss.00042.jats
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<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN"
"JATS-publishing1.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
<journal-title>Journal of Open Source Software</journal-title>
<abbrev-journal-title>JOSS</abbrev-journal-title>
</journal-title-group>
<issn publication-format="electronic">2475-9066</issn>
<publisher>
<publisher-name>Open Journals</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">42</article-id>
<article-id pub-id-type="doi">10.21105/joss.00042</article-id>
<title-group>
<article-title>Gillespie.jl: Stochastic Simulation Algorithm in
Julia</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">0000-0002-5207-9879</contrib-id>
<string-name>Simon DW Frost</string-name>
<xref ref-type="aff" rid="aff-1"/>
</contrib>
<aff id="aff-1">
<institution-wrap>
<institution>University of Cambridge</institution>
</institution-wrap>
</aff>
</contrib-group>
<pub-date date-type="pub" publication-format="electronic" iso-8601-date="2016-07-18">
<day>18</day>
<month>7</month>
<year>2016</year>
</pub-date>
<volume>1</volume>
<issue>3</issue>
<fpage>42</fpage>
<permissions>
<copyright-statement>Authors of papers retain copyright and release the
work under a Creative Commons Attribution 4.0 International License (CC
BY 4.0)</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>The article authors</copyright-holder>
<license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
<license-p>Authors of papers retain copyright and release the work under
a Creative Commons Attribution 4.0 International License (CC BY
4.0)</license-p>
</license>
</permissions>
<kwd-group kwd-group-type="author">
<kwd>stochastic simulation</kwd>
<kwd>Doob-Gillespie algorithm</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="summary">
<title>Summary</title>
<p><monospace>Gillespie.jl</monospace>
(<xref alt="Frost, 2016" rid="ref-GillespieJL" ref-type="bibr">Frost,
2016</xref>) is a Julia package for stochastic simulation using
Gillespie’s direct method (sometimes called the Doob-Gillespie
algorithm)
(<xref alt="Doob, 1945" rid="ref-Doob1945" ref-type="bibr">Doob,
1945</xref>;
<xref alt="Gillespie, 1977" rid="ref-Gillespie1977" ref-type="bibr">Gillespie,
1977</xref>), 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
<monospace>GillespieSSA</monospace> by Mario Pineda-Krch
(<xref alt="Pineda-Krch, 2008" rid="ref-Pineda-Krch2008" ref-type="bibr">Pineda-Krch,
2008</xref>), although <monospace>Gillespie.jl</monospace> only
implements the standard exact method at present, whereas
<monospace>GillespieSSA</monospace> also includes other methods, such
as tau-leaping, <italic>etc.</italic>.
<monospace>Gillespie.jl</monospace> is intended to offer performance
on par with hand-coded C code, while maintaining a simple but flexible
interface.</p>
</sec>
</body>
<back>
<ref-list>
<ref-list>
<ref id="ref-Doob1945">
<element-citation publication-type="article-journal">
<person-group person-group-type="author">
<name><surname>Doob</surname><given-names>Joseph L</given-names></name>
</person-group>
<article-title>Markoff chains–denumerable case</article-title>
<source>Transactions of the American Mathematical Society</source>
<publisher-name>JSTOR</publisher-name>
<year iso-8601-date="1945">1945</year>
<volume>58</volume>
<issue>3</issue>
<uri>http://www.jstor.org/stable/1990339</uri>
<pub-id pub-id-type="doi">10.2307/1990339</pub-id>
</element-citation>
</ref>
<ref id="ref-GillespieJL">
<element-citation publication-type="webpage">
<person-group person-group-type="author">
<name><surname>Frost</surname><given-names>Simon D. W.</given-names></name>
</person-group>
<article-title>Gillespie.jl: Stochastic simulation in julia</article-title>
<year iso-8601-date="2016">2016</year>
<date-in-citation content-type="access-date"><year iso-8601-date="2016-02-14">2016</year><month>02</month><day>14</day></date-in-citation>
<uri>https://github.com/sdwfrost/Gillespie.jl</uri>
</element-citation>
</ref>
<ref id="ref-Gillespie1977">
<element-citation publication-type="article-journal">
<person-group person-group-type="author">
<name><surname>Gillespie</surname><given-names>Daniel T</given-names></name>
</person-group>
<article-title>Exact stochastic simulation of coupled chemical reactions</article-title>
<source>The journal of physical chemistry</source>
<publisher-name>ACS Publications</publisher-name>
<year iso-8601-date="1977">1977</year>
<volume>81</volume>
<issue>25</issue>
<uri>http://pubs.acs.org/doi/pdf/10.1021/j100540a008</uri>
<pub-id pub-id-type="doi">10.1021/j100540a008</pub-id>
</element-citation>
</ref>
<ref id="ref-Pineda-Krch2008">
<element-citation publication-type="article-journal">
<person-group person-group-type="author">
<name><surname>Pineda-Krch</surname><given-names>Mario</given-names></name>
</person-group>
<article-title>GillespieSSA: Stochastic simulation algorithm in r</article-title>
<source>Journal of Statistical Software</source>
<year iso-8601-date="2008">2008</year>
<volume>25</volume>
<uri>https://www.jstatsoft.org/article/view/v025i12</uri>
<pub-id pub-id-type="doi">10.18637/jss.v025.i12</pub-id>
</element-citation>
</ref>
</ref-list>
</ref-list>
</back>
</article>