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 specif...

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Bibliographic Details
Published in:Journal of integrative bioinformatics 2023-03, Vol.20 (1)
Main Authors: Schaff, James C., Lakshminarayana, Anuradha, Murphy, Robert F., Bergmann, Frank T., Funahashi, Akira, Sullivan, Devin P., Smith, Lucian P.
Format: Article
Language:English
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Summary: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 specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML to extend the Core specification and add additional syntactic constructs. The SBML 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.
ISSN:1613-4516
1613-4516
DOI:10.1515/jib-2022-0054