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MomentClosure.jl: automated moment closure approximations in Julia

SUMMARY: 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 biochemi...

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Detalles Bibliográficos
Autores principales: Sukys, Augustinas, Grima, Ramon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696096/
https://www.ncbi.nlm.nih.gov/pubmed/34170295
http://dx.doi.org/10.1093/bioinformatics/btab469
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author Sukys, Augustinas
Grima, Ramon
author_facet Sukys, Augustinas
Grima, Ramon
author_sort Sukys, Augustinas
collection PubMed
description SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: MomentClosure.jl is freely accessible under the MIT licence. Source code and documentation are available at https://github.com/augustinas1/MomentClosure.jl.
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spelling pubmed-86960962022-01-04 MomentClosure.jl: automated moment closure approximations in Julia Sukys, Augustinas Grima, Ramon Bioinformatics Applications Notes SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: MomentClosure.jl is freely accessible under the MIT licence. Source code and documentation are available at https://github.com/augustinas1/MomentClosure.jl. Oxford University Press 2021-06-25 /pmc/articles/PMC8696096/ /pubmed/34170295 http://dx.doi.org/10.1093/bioinformatics/btab469 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Sukys, Augustinas
Grima, Ramon
MomentClosure.jl: automated moment closure approximations in Julia
title MomentClosure.jl: automated moment closure approximations in Julia
title_full MomentClosure.jl: automated moment closure approximations in Julia
title_fullStr MomentClosure.jl: automated moment closure approximations in Julia
title_full_unstemmed MomentClosure.jl: automated moment closure approximations in Julia
title_short MomentClosure.jl: automated moment closure approximations in Julia
title_sort momentclosure.jl: automated moment closure approximations in julia
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696096/
https://www.ncbi.nlm.nih.gov/pubmed/34170295
http://dx.doi.org/10.1093/bioinformatics/btab469
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