{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T20:52:39Z","timestamp":1772052759769,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,6,25]],"date-time":"2021-06-25T00:00:00Z","timestamp":1624579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Alan Turing Institute Doctoral Studentship [EPSRC","award":["EP\/N510129\/1"],"award-info":[{"award-number":["EP\/N510129\/1"]}]},{"DOI":"10.13039\/501100000275","name":"Leverhulme Trust","doi-asserted-by":"publisher","award":["RPG-2018-423"],"award-info":[{"award-number":["RPG-2018-423"]}],"id":[{"id":"10.13039\/501100000275","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>MomentClosure.jl is a Julia package providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. It extends the capabilities of modelling stochastic biochemical systems in Julia and can be particularly useful when exact analytic solutions of the chemical master equation are unavailable and when Monte Carlo simulations are computationally expensive.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MomentClosure.jl is freely accessible under the MIT licence. Source code and documentation are available at https:\/\/github.com\/augustinas1\/MomentClosure.jl.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab469","type":"journal-article","created":{"date-parts":[[2021,6,22]],"date-time":"2021-06-22T11:10:20Z","timestamp":1624360220000},"page":"289-290","source":"Crossref","is-referenced-by-count":13,"title":["MomentClosure.jl: automated moment closure approximations in Julia"],"prefix":"10.1093","volume":"38","author":[{"given":"Augustinas","family":"Sukys","sequence":"first","affiliation":[{"name":"SynthSys, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3JD, UK"},{"name":"The Alan Turing Institute , London NW1 2DB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1266-8169","authenticated-orcid":false,"given":"Ramon","family":"Grima","sequence":"additional","affiliation":[{"name":"SynthSys, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3JD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,6,25]]},"reference":[{"key":"2023020108384663000_btab469-B1","doi-asserted-by":"crossref","first-page":"174101","DOI":"10.1063\/1.4802475","article-title":"A general moment expansion method for stochastic kinetic models","volume":"138","author":"Ale","year":"2013","journal-title":"J. Chem. Phys"},{"key":"2023020108384663000_btab469-B2","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1049\/iet-syb.2011.0013","article-title":"Mass fluctuation kinetics: analysis and computation of equilibria and local dynamics","volume":"5","author":"Azunre","year":"2011","journal-title":"IET Syst. Biol"},{"key":"2023020108384663000_btab469-B3","doi-asserted-by":"crossref","first-page":"20180967","DOI":"10.1098\/rsif.2018.0967","article-title":"Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data","volume":"16","author":"Cao","year":"2019","journal-title":"J. R. Soc. Interf"},{"key":"2023020108384663000_btab469-B4","doi-asserted-by":"crossref","first-page":"2863","DOI":"10.1093\/bioinformatics\/btw229","article-title":"MEANS: python package for moment expansion approximation, iNference and simulation","volume":"32","author":"Fan","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020108384663000_btab469-B5","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1049\/iet-syb:20070031","article-title":"Moment-closure approximations for mass-action models","volume":"3","author":"Gillespie","year":"2009","journal-title":"IET Syst. Biol"},{"key":"2023020108384663000_btab469-B6","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"Gillespie","year":"1977","journal-title":"J. Phys. Chem"},{"key":"2023020108384663000_btab469-B7","first-page":"142","author":"Hespanha","year":"2008"},{"key":"2023020108384663000_btab469-B8","doi-asserted-by":"crossref","first-page":"e0146732","DOI":"10.1371\/journal.pone.0146732","article-title":"CERENA: ChEmical REaction Network Analyzer\u2014a toolbox for the simulation and analysis of stochastic chemical kinetics","volume":"11","author":"Kazeroonian","year":"2016","journal-title":"PLoS One"},{"key":"2023020108384663000_btab469-B9","doi-asserted-by":"crossref","first-page":"094107","DOI":"10.1063\/1.4929837","article-title":"Multivariate moment closure techniques for stochastic kinetic models","volume":"143","author":"Lakatos","year":"2015","journal-title":"J. Chem. Phys"},{"key":"2023020108384663000_btab469-B10","first-page":"785","article-title":"A moment closure method for stochastic chemical reaction networks with general kinetics","volume":"70","author":"Lee","year":"2013","journal-title":"MATCH Commun. Math. Comput. Chem"},{"key":"2023020108384663000_btab469-B11","author":"Ma","year":"2021"},{"key":"2023020108384663000_btab469-B12","first-page":"btab058","article-title":"Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations","author":"Pietzsch","year":"2021","journal-title":"Bioinformatics"},{"key":"2023020108384663000_btab469-B13","article-title":"DifferentialEquations.jl\u2013a performant and feature-rich ecosystem for solving differential equations in Julia","volume":"5, 15","author":"Rackauckas","year":"2017","journal-title":"J. Open Res. Software"},{"key":"2023020108384663000_btab469-B14","doi-asserted-by":"crossref","first-page":"185101","DOI":"10.1063\/1.4934990","article-title":"Comparison of different moment-closure approximations for stochastic chemical kinetics","volume":"143","author":"Schnoerr","year":"2015","journal-title":"J. Chem. Phys"},{"key":"2023020108384663000_btab469-B15","doi-asserted-by":"crossref","first-page":"093001","DOI":"10.1088\/1751-8121\/aa54d9","article-title":"Approximation and inference methods for stochastic biochemical kinetics\u2014a tutorial review","volume":"50","author":"Schnoerr","year":"2017","journal-title":"J. Phys. A: Math. Theor"},{"key":"2023020108384663000_btab469-B16","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1109\/TBCAS.2015.2453158","article-title":"Conditional moment closure schemes for studying stochastic dynamics of genetic circuits","volume":"9","author":"Soltani","year":"2015","journal-title":"IEEE Trans. Biomed. Circuits Syst"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab469\/39309771\/btab469.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/289\/49006428\/btab469.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/289\/49006428\/btab469.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:54:03Z","timestamp":1675281243000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/1\/289\/6309452"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,6,25]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab469","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,6,25]]}}}