build based on a2717c7

dev/index.html

@@ -13,4 +13,4 @@
     doi = {10.1093/bioinformatics/btab469},
     url = {https://doi.org/10.1093/bioinformatics/btab469},
     eprint = {https://academic.oup.com/bioinformatics/article-pdf/38/1/289/41891091/btab469.pdf},
-}</code></pre><h2 id="References"><a class="docs-heading-anchor" href="#References">References</a><a id="References-1"></a><a class="docs-heading-anchor-permalink" href="#References" title="Permalink"></a></h2><p>[1]: D. Schnoerr, G. Sanguinetti, and R. Grima, &quot;Approximation and inference methods for stochastic biochemical kinetics - a tutorial review&quot;, Journal of Physics A: Mathematical and Theoretical 50, 093001 (2017). <a href="https://doi.org/10.1088/1751-8121/aa54d9">https://doi.org/10.1088/1751-8121/aa54d9</a></p><p>[2]: A. Ale, P. Kirk, and M. P. H. Stumpf, &quot;A general moment expansion method for stochastic kinetic models&quot;, The Journal of Chemical Physics 138, 174101 (2013). <a href="https://doi.org/10.1063/1.4802475">https://doi.org/10.1063/1.4802475</a></p><p>[3]: C. H. Lee, &quot;A Moment Closure Method for Stochastic Chemical Reaction Networks with General Kinetics&quot;, MATCH Communications in Mathematical and in Computer Chemistry 70, 785-800 (2013). <a href="https://match.pmf.kg.ac.rs/electronic_versions/Match70/n3/match70n3_785-800.pdf">https://match.pmf.kg.ac.rs/electronic<em>versions/Match70/n3/match70n3</em>785-800.pdf</a></p><p>[4]: D. Schnoerr, G. Sanguinetti, and R. Grima, &quot;Comparison of different moment-closure approximations for stochastic chemical kinetics&quot;, The Journal of Chemical Physics 143, 185101 (2015). <a href="https://doi.org/10.1063/1.4934990">https://doi.org/10.1063/1.4934990</a></p><p>[5]: E. Lakatos, A. Ale, P. D. W. Kirk, and M. P. H. Stumpf, &quot;Multivariate moment closure techniques for stochastic kinetic models&quot;, The Journal of Chemical Physics 143, 094107 (2015). <a href="https://doi.org/10.1063/1.4929837">https://doi.org/10.1063/1.4929837</a></p><p>[6]: A. Singh and J. P. Hespanha, &quot;Lognormal Moment Closures for Biochemical Reactions&quot;, in Proceedings of the 45th IEEE Conference on Decision and Control, ISSN: 0191-2216 (Dec. 2006), pp. 2063-2068. <a href="https://doi.org/10.1109/CDC.2006.376994">https://doi.org/10.1109/CDC.2006.376994</a></p><p>[7]: M. Soltani, C. A. Vargas-Garcia, and A. Singh, &quot;Conditional Moment Closure Schemes for Studying Stochastic Dynamics of Genetic Circuits&quot;, IEEE Transactions on Biomedical Circuits and Systems 9, 518-526 (2015). <a href="https://doi.org/10.1109/TBCAS.2015.2453158">https://doi.org/10.1109/TBCAS.2015.2453158</a></p><p>[8]: Z. Cao and R. Grima, &quot;Linear mapping approximation of gene regulatory networks with stochastic dynamics&quot;, Nature Communications 9, 3305 (2018). <a href="https://doi.org/10.1038/s41467-018-05822-0">https://doi.org/10.1038/s41467-018-05822-0</a></p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="theory/moment_expansion_CME/">Moment Expansion (CME) »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Saturday 6 May 2023 00:49">Saturday 6 May 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+}</code></pre><h2 id="References"><a class="docs-heading-anchor" href="#References">References</a><a id="References-1"></a><a class="docs-heading-anchor-permalink" href="#References" title="Permalink"></a></h2><p>[1]: D. Schnoerr, G. Sanguinetti, and R. Grima, &quot;Approximation and inference methods for stochastic biochemical kinetics - a tutorial review&quot;, Journal of Physics A: Mathematical and Theoretical 50, 093001 (2017). <a href="https://doi.org/10.1088/1751-8121/aa54d9">https://doi.org/10.1088/1751-8121/aa54d9</a></p><p>[2]: A. Ale, P. Kirk, and M. P. H. Stumpf, &quot;A general moment expansion method for stochastic kinetic models&quot;, The Journal of Chemical Physics 138, 174101 (2013). <a href="https://doi.org/10.1063/1.4802475">https://doi.org/10.1063/1.4802475</a></p><p>[3]: C. H. Lee, &quot;A Moment Closure Method for Stochastic Chemical Reaction Networks with General Kinetics&quot;, MATCH Communications in Mathematical and in Computer Chemistry 70, 785-800 (2013). <a href="https://match.pmf.kg.ac.rs/electronic_versions/Match70/n3/match70n3_785-800.pdf">https://match.pmf.kg.ac.rs/electronic<em>versions/Match70/n3/match70n3</em>785-800.pdf</a></p><p>[4]: D. Schnoerr, G. Sanguinetti, and R. Grima, &quot;Comparison of different moment-closure approximations for stochastic chemical kinetics&quot;, The Journal of Chemical Physics 143, 185101 (2015). <a href="https://doi.org/10.1063/1.4934990">https://doi.org/10.1063/1.4934990</a></p><p>[5]: E. Lakatos, A. Ale, P. D. W. Kirk, and M. P. H. Stumpf, &quot;Multivariate moment closure techniques for stochastic kinetic models&quot;, The Journal of Chemical Physics 143, 094107 (2015). <a href="https://doi.org/10.1063/1.4929837">https://doi.org/10.1063/1.4929837</a></p><p>[6]: A. Singh and J. P. Hespanha, &quot;Lognormal Moment Closures for Biochemical Reactions&quot;, in Proceedings of the 45th IEEE Conference on Decision and Control, ISSN: 0191-2216 (Dec. 2006), pp. 2063-2068. <a href="https://doi.org/10.1109/CDC.2006.376994">https://doi.org/10.1109/CDC.2006.376994</a></p><p>[7]: M. Soltani, C. A. Vargas-Garcia, and A. Singh, &quot;Conditional Moment Closure Schemes for Studying Stochastic Dynamics of Genetic Circuits&quot;, IEEE Transactions on Biomedical Circuits and Systems 9, 518-526 (2015). <a href="https://doi.org/10.1109/TBCAS.2015.2453158">https://doi.org/10.1109/TBCAS.2015.2453158</a></p><p>[8]: Z. Cao and R. Grima, &quot;Linear mapping approximation of gene regulatory networks with stochastic dynamics&quot;, Nature Communications 9, 3305 (2018). <a href="https://doi.org/10.1038/s41467-018-05822-0">https://doi.org/10.1038/s41467-018-05822-0</a></p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="theory/moment_expansion_CME/">Moment Expansion (CME) »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 4 September 2023 23:58">Monday 4 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/search/index.html

@@ -1,2 +1,2 @@
 <!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · MomentClosure.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link rel="canonical" href="https://augustinas1.github.io/MomentClosure.jl/search/"/><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">MomentClosure.jl</a></span></div><form class="docs-search" action><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><span class="tocitem">Theory</span><ul><li><a class="tocitem" href="../theory/moment_expansion_CME/">Moment Expansion (CME)</a></li><li><a class="tocitem" href="../theory/moment_expansion_SDE/">Moment Expansion (SDE)</a></li><li><a class="tocitem" href="../theory/moment_closure_approximations/">Moment Closure Approximations</a></li><li><a class="tocitem" href="../theory/linear_mapping_approximation/">Linear Mapping Approximation</a></li></ul></li><li><span class="tocitem">Tutorials</span><ul><li><a class="tocitem" href="../tutorials/using_momentclosure/">Using MomentClosure</a></li><li><a class="tocitem" href="../tutorials/using_momentclosure_SDE/">Moment Equations from SDEs</a></li><li><a class="tocitem" href="../tutorials/common_issues/">Common Issues</a></li><li><a class="tocitem" href="../tutorials/time-dependent_propensities/">Time-dependent Propensity Functions</a></li><li><a class="tocitem" href="../tutorials/geometric_reactions+conditional_closures/">Geometrically Distributed Reaction Products and Conditional Closures</a></li><li><a class="tocitem" href="../tutorials/P53_system_example/">P53 System Example</a></li><li><a class="tocitem" href="../tutorials/derivative_matching_example/">Derivative Matching Example</a></li><li><a class="tocitem" href="../tutorials/SIR_example/">SIR Model Example</a></li><li><a class="tocitem" href="../tutorials/LMA_example/">LMA Example</a></li><li><a class="tocitem" href="../tutorials/parameter_estimation_SDE/">Parameter Estimation of Diffusion Processes</a></li></ul></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../api/momentclosure_api/">MomentClosure.jl API</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Saturday 6 May 2023 00:49">Saturday 6 May 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · MomentClosure.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link rel="canonical" href="https://augustinas1.github.io/MomentClosure.jl/search/"/><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">MomentClosure.jl</a></span></div><form class="docs-search" action><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><span class="tocitem">Theory</span><ul><li><a class="tocitem" href="../theory/moment_expansion_CME/">Moment Expansion (CME)</a></li><li><a class="tocitem" href="../theory/moment_expansion_SDE/">Moment Expansion (SDE)</a></li><li><a class="tocitem" href="../theory/moment_closure_approximations/">Moment Closure Approximations</a></li><li><a class="tocitem" href="../theory/linear_mapping_approximation/">Linear Mapping Approximation</a></li></ul></li><li><span class="tocitem">Tutorials</span><ul><li><a class="tocitem" href="../tutorials/using_momentclosure/">Using MomentClosure</a></li><li><a class="tocitem" href="../tutorials/using_momentclosure_SDE/">Moment Equations from SDEs</a></li><li><a class="tocitem" href="../tutorials/common_issues/">Common Issues</a></li><li><a class="tocitem" href="../tutorials/time-dependent_propensities/">Time-dependent Propensity Functions</a></li><li><a class="tocitem" href="../tutorials/geometric_reactions+conditional_closures/">Geometrically Distributed Reaction Products and Conditional Closures</a></li><li><a class="tocitem" href="../tutorials/P53_system_example/">P53 System Example</a></li><li><a class="tocitem" href="../tutorials/derivative_matching_example/">Derivative Matching Example</a></li><li><a class="tocitem" href="../tutorials/SIR_example/">SIR Model Example</a></li><li><a class="tocitem" href="../tutorials/LMA_example/">LMA Example</a></li><li><a class="tocitem" href="../tutorials/parameter_estimation_SDE/">Parameter Estimation of Diffusion Processes</a></li></ul></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../api/momentclosure_api/">MomentClosure.jl API</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 4 September 2023 23:58">Monday 4 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>