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BY 4.0 license Open Access Published by De Gruyter March 10, 2023

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

  • James C. Schaff ORCID logo , Anuradha Lakshminarayana , Robert F. Murphy ORCID logo , Frank T. Bergmann ORCID logo , Akira Funahashi ORCID logo , Devin P. Sullivan ORCID logo and Lucian P. Smith ORCID logo EMAIL logo


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.

Corresponding author: Lucian P. Smith, University of Washington, Seattle, WA, USA, E-mail:

Received: 2022-10-28
Revised: 2021-01-10
Accepted: 2023-02-13
Published Online: 2023-03-10

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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