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CellML metadata standards, associated tools and repositories

The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and...

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Detalles Bibliográficos
Autores principales: Beard, Daniel A., Britten, Randall, Cooling, Mike T., Garny, Alan, Halstead, Matt D.B., Hunter, Peter J., Lawson, James, Lloyd, Catherine M., Marsh, Justin, Miller, Andrew, Nickerson, David P., Nielsen, Poul M.F., Nomura, Taishin, Subramanium, Shankar, Wimalaratne, Sarala M., Yu, Tommy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268215/
https://www.ncbi.nlm.nih.gov/pubmed/19380315
http://dx.doi.org/10.1098/rsta.2008.0310
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author Beard, Daniel A.
Britten, Randall
Cooling, Mike T.
Garny, Alan
Halstead, Matt D.B.
Hunter, Peter J.
Lawson, James
Lloyd, Catherine M.
Marsh, Justin
Miller, Andrew
Nickerson, David P.
Nielsen, Poul M.F.
Nomura, Taishin
Subramanium, Shankar
Wimalaratne, Sarala M.
Yu, Tommy
author_facet Beard, Daniel A.
Britten, Randall
Cooling, Mike T.
Garny, Alan
Halstead, Matt D.B.
Hunter, Peter J.
Lawson, James
Lloyd, Catherine M.
Marsh, Justin
Miller, Andrew
Nickerson, David P.
Nielsen, Poul M.F.
Nomura, Taishin
Subramanium, Shankar
Wimalaratne, Sarala M.
Yu, Tommy
author_sort Beard, Daniel A.
collection PubMed
description The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website.
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spelling pubmed-32682152012-01-31 CellML metadata standards, associated tools and repositories Beard, Daniel A. Britten, Randall Cooling, Mike T. Garny, Alan Halstead, Matt D.B. Hunter, Peter J. Lawson, James Lloyd, Catherine M. Marsh, Justin Miller, Andrew Nickerson, David P. Nielsen, Poul M.F. Nomura, Taishin Subramanium, Shankar Wimalaratne, Sarala M. Yu, Tommy Philos Trans A Math Phys Eng Sci Articles The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website. The Royal Society 2009-05-28 /pmc/articles/PMC3268215/ /pubmed/19380315 http://dx.doi.org/10.1098/rsta.2008.0310 Text en Copyright © 2009 The Royal Society http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Beard, Daniel A.
Britten, Randall
Cooling, Mike T.
Garny, Alan
Halstead, Matt D.B.
Hunter, Peter J.
Lawson, James
Lloyd, Catherine M.
Marsh, Justin
Miller, Andrew
Nickerson, David P.
Nielsen, Poul M.F.
Nomura, Taishin
Subramanium, Shankar
Wimalaratne, Sarala M.
Yu, Tommy
CellML metadata standards, associated tools and repositories
title CellML metadata standards, associated tools and repositories
title_full CellML metadata standards, associated tools and repositories
title_fullStr CellML metadata standards, associated tools and repositories
title_full_unstemmed CellML metadata standards, associated tools and repositories
title_short CellML metadata standards, associated tools and repositories
title_sort cellml metadata standards, associated tools and repositories
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268215/
https://www.ncbi.nlm.nih.gov/pubmed/19380315
http://dx.doi.org/10.1098/rsta.2008.0310
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