Hybrid models and biological model reduction with PyDSTool.

The PyDSTool software environment is designed to develop, simulate, and analyze dynamical systems models, particularly for biological applications. Unlike the engineering application focus and graphical specification environments of most general purpose simulation tools, PyDSTool provides a programm...

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Autor principal:	Robert Clewley
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b6f1846b7902413fbc00f60ba4b41c32
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spelling	oai:doaj.org-article:b6f1846b7902413fbc00f60ba4b41c322021-11-18T05:51:07ZHybrid models and biological model reduction with PyDSTool.1553-734X1553-735810.1371/journal.pcbi.1002628https://doaj.org/article/b6f1846b7902413fbc00f60ba4b41c322012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22912566/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The PyDSTool software environment is designed to develop, simulate, and analyze dynamical systems models, particularly for biological applications. Unlike the engineering application focus and graphical specification environments of most general purpose simulation tools, PyDSTool provides a programmatic environment well suited to exploratory data- and hypothesis-driven biological modeling problems. In this work, we show how the environment facilitates the application of hybrid dynamical modeling to the reverse engineering of complex biophysical dynamics; in this case, of an excitable membrane. The example demonstrates how the software provides novel tools that support the inference and validation of mechanistic hypotheses and the inclusion of data constraints in both quantitative and qualitative ways. The biophysical application is broadly relevant to models in the biosciences. The open source and platform-independent PyDSTool package is freely available under the BSD license from http://sourceforge.net/projects/pydstool/. The hosting service provides links to documentation and online forums for user support.Robert ClewleyPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 8, p e1002628 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Robert Clewley Hybrid models and biological model reduction with PyDSTool.
description	The PyDSTool software environment is designed to develop, simulate, and analyze dynamical systems models, particularly for biological applications. Unlike the engineering application focus and graphical specification environments of most general purpose simulation tools, PyDSTool provides a programmatic environment well suited to exploratory data- and hypothesis-driven biological modeling problems. In this work, we show how the environment facilitates the application of hybrid dynamical modeling to the reverse engineering of complex biophysical dynamics; in this case, of an excitable membrane. The example demonstrates how the software provides novel tools that support the inference and validation of mechanistic hypotheses and the inclusion of data constraints in both quantitative and qualitative ways. The biophysical application is broadly relevant to models in the biosciences. The open source and platform-independent PyDSTool package is freely available under the BSD license from http://sourceforge.net/projects/pydstool/. The hosting service provides links to documentation and online forums for user support.
format	article
author	Robert Clewley
author_facet	Robert Clewley
author_sort	Robert Clewley
title	Hybrid models and biological model reduction with PyDSTool.
title_short	Hybrid models and biological model reduction with PyDSTool.
title_full	Hybrid models and biological model reduction with PyDSTool.
title_fullStr	Hybrid models and biological model reduction with PyDSTool.
title_full_unstemmed	Hybrid models and biological model reduction with PyDSTool.
title_sort	hybrid models and biological model reduction with pydstool.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/b6f1846b7902413fbc00f60ba4b41c32
work_keys_str_mv	AT robertclewley hybridmodelsandbiologicalmodelreductionwithpydstool
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Hybrid models and biological model reduction with PyDSTool.

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