Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.

Integrating computer simulation with conventional wet-lab research has proven to have much potential in furthering the understanding of biological systems. Success requires the relationship between simulation and the real-world system to be established: substantial aspects of the biological system a...

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Autores principales:	Kieran Alden, Mark Read, Jon Timmis, Paul S Andrews, Henrique Veiga-Fernandes, Mark Coles
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/66f38c7de0104754bbb304d64e8e893e
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id	oai:doaj.org-article:66f38c7de0104754bbb304d64e8e893e
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spelling	oai:doaj.org-article:66f38c7de0104754bbb304d64e8e893e2021-11-18T05:52:25ZSpartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.1553-734X1553-735810.1371/journal.pcbi.1002916https://doaj.org/article/66f38c7de0104754bbb304d64e8e893e2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23468606/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Integrating computer simulation with conventional wet-lab research has proven to have much potential in furthering the understanding of biological systems. Success requires the relationship between simulation and the real-world system to be established: substantial aspects of the biological system are typically unknown, and the abstract nature of simulation can complicate interpretation of in silico results in terms of the biology. Here we present spartan (Simulation Parameter Analysis RToolkit ApplicatioN), a package of statistical techniques specifically designed to help researchers understand this relationship and provide novel biological insight. The tools comprising spartan help identify which simulation results can be attributed to the dynamics of the modelled biological system, rather than artefacts of biological uncertainty or parametrisation, or simulation stochasticity. Statistical analyses reveal the influence that pathways and components have on simulation behaviour, offering valuable biological insight into aspects of the system under study. We demonstrate the power of spartan in providing critical insight into aspects of lymphoid tissue development in the small intestine through simulation. Spartan is released under a GPLv2 license, implemented within the open source R statistical environment, and freely available from both the Comprehensive R Archive Network (CRAN) and http://www.cs.york.ac.uk/spartan. The techniques within the package can be applied to traditional ordinary or partial differential equation simulations as well as agent-based implementations. Manuals, comprehensive tutorials, and example simulation data upon which spartan can be applied are available from the website.Kieran AldenMark ReadJon TimmisPaul S AndrewsHenrique Veiga-FernandesMark ColesPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 2, p e1002916 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Kieran Alden Mark Read Jon Timmis Paul S Andrews Henrique Veiga-Fernandes Mark Coles Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
description	Integrating computer simulation with conventional wet-lab research has proven to have much potential in furthering the understanding of biological systems. Success requires the relationship between simulation and the real-world system to be established: substantial aspects of the biological system are typically unknown, and the abstract nature of simulation can complicate interpretation of in silico results in terms of the biology. Here we present spartan (Simulation Parameter Analysis RToolkit ApplicatioN), a package of statistical techniques specifically designed to help researchers understand this relationship and provide novel biological insight. The tools comprising spartan help identify which simulation results can be attributed to the dynamics of the modelled biological system, rather than artefacts of biological uncertainty or parametrisation, or simulation stochasticity. Statistical analyses reveal the influence that pathways and components have on simulation behaviour, offering valuable biological insight into aspects of the system under study. We demonstrate the power of spartan in providing critical insight into aspects of lymphoid tissue development in the small intestine through simulation. Spartan is released under a GPLv2 license, implemented within the open source R statistical environment, and freely available from both the Comprehensive R Archive Network (CRAN) and http://www.cs.york.ac.uk/spartan. The techniques within the package can be applied to traditional ordinary or partial differential equation simulations as well as agent-based implementations. Manuals, comprehensive tutorials, and example simulation data upon which spartan can be applied are available from the website.
format	article
author	Kieran Alden Mark Read Jon Timmis Paul S Andrews Henrique Veiga-Fernandes Mark Coles
author_facet	Kieran Alden Mark Read Jon Timmis Paul S Andrews Henrique Veiga-Fernandes Mark Coles
author_sort	Kieran Alden
title	Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
title_short	Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
title_full	Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
title_fullStr	Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
title_full_unstemmed	Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
title_sort	spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/66f38c7de0104754bbb304d64e8e893e
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Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.

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