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SBML level 3 package: spatial processes, version 1, release 1

While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments. The SBML L...

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Autores principales: Schaff, James C., Lakshminarayana, Anuradha, Murphy, Robert F., Bergmann, Frank T., Funahashi, Akira, Sullivan, Devin P., Smith, Lucian P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: De Gruyter 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063174/
http://dx.doi.org/10.1515/jib-2022-0054
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author Schaff, James C.
Lakshminarayana, Anuradha
Murphy, Robert F.
Bergmann, Frank T.
Funahashi, Akira
Sullivan, Devin P.
Smith, Lucian P.
author_facet Schaff, James C.
Lakshminarayana, Anuradha
Murphy, Robert F.
Bergmann, Frank T.
Funahashi, Akira
Sullivan, Devin P.
Smith, Lucian P.
author_sort Schaff, James C.
collection PubMed
description While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments. The SBML Level 3 Core specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Spatial Processes package for SBML Level 3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes.
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spelling pubmed-100631742023-03-31 SBML level 3 package: spatial processes, version 1, release 1 Schaff, James C. Lakshminarayana, Anuradha Murphy, Robert F. Bergmann, Frank T. Funahashi, Akira Sullivan, Devin P. Smith, Lucian P. J Integr Bioinform Article While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments. The SBML Level 3 Core specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Spatial Processes package for SBML Level 3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes. De Gruyter 2023-03-10 /pmc/articles/PMC10063174/ http://dx.doi.org/10.1515/jib-2022-0054 Text en © 2023 the author(s), published by De Gruyter, Berlin/Boston https://creativecommons.org/licenses/by/4.0/This work is licensed under the Creative Commons Attribution 4.0 International License.
spellingShingle Article
Schaff, James C.
Lakshminarayana, Anuradha
Murphy, Robert F.
Bergmann, Frank T.
Funahashi, Akira
Sullivan, Devin P.
Smith, Lucian P.
SBML level 3 package: spatial processes, version 1, release 1
title SBML level 3 package: spatial processes, version 1, release 1
title_full SBML level 3 package: spatial processes, version 1, release 1
title_fullStr SBML level 3 package: spatial processes, version 1, release 1
title_full_unstemmed SBML level 3 package: spatial processes, version 1, release 1
title_short SBML level 3 package: spatial processes, version 1, release 1
title_sort sbml level 3 package: spatial processes, version 1, release 1
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063174/
http://dx.doi.org/10.1515/jib-2022-0054
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