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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
De Gruyter
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063174/ http://dx.doi.org/10.1515/jib-2022-0054 |
_version_ | 1785017653894578176 |
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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. |
format | Online Article Text |
id | pubmed-10063174 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | De Gruyter |
record_format | MEDLINE/PubMed |
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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