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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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.
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container_title Journal of integrative bioinformatics
container_volume 20
creator Schaff, James C.
Lakshminarayana, Anuradha
Murphy, Robert F.
Bergmann, Frank T.
Funahashi, Akira
Sullivan, Devin P.
Smith, Lucian P.
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 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.
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title SBML level 3 package: spatial processes, version 1, release 1
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