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Spatial Geometries and Spatial Processes

SBML Level 3 Package Activity Status Page

Please note: This page is for the proposal of this SBML Level 3 package.
Information on this page is likely to be out of date with current developments.
Current development is focused on the specification of this package.
Specification activity is described on a separate page.

Package objectives

The goal of supporting spatial characteristics in SBML Level 3 is to allow the representation of the geometric features of compartments and the spatial distribution of model quantities and processes. Today, SBML models are nonspatial: compartments are topological structures only, with dimensionality, size and (in earlier Levels/Versions of SBML) containment, being their only physical attributes. This was partly a conscious design decision, because there are far more nonspatial modeling tools available and so our priorities went towards that. However, it is clearly insufficient for many potential modeling uses, including the problems described above. Today there are a number of computational modeling systems supporting spatial characteristics in biochemical network models.

The focus of the spatial features effort is on extending SBML to support representing at least the following: (1) the size and shape of physical entities, whether compartments or reacting species; (2) the absolute or relative spatial location of reacting species in compartments, for instance in a volume, on membrane surfaces, or along microtubules; (3) the rates of diffusion of species through compartments; and (4) the definition of rate equations and algebraic constraints describing phenomena either at specific locations, or distributed across compartments.

The short label for this package is spatial.

Package specifications

A separate page is dedicated to the specification development activities involving this package.

Package proposals

The SBML Development Process for SBML Level 3 defines two stages: a proposal stage, and a specification development stage. The following is a list of the active proposals for the spatial modeling area of SBML Level 3:

Proposal name or identification Date Comments
Spatial proposal by James C. Schaff (2011) 2011 (3)

Legend for editorial comments:
(1) Proposal has not yet been structured according to the recommended format for SBML Level 3 package proposals.
(2) Proposal needs to be updated for SBML Level 3.
(3) Work in progress—the authors have not finalized this proposal.

Package Working Group (PWG)

After a vote by the SBML community to accept the above proposal as something that addresses a valid need and takes a reasonable approach, we formed a working group to help complete the proposal and resolve any implementation issues that might arise. Membership of this group is open to all interested members of the SBML community; all you need to do is sign up for the sbml-spatial mailing list.

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This page was last modified 02:51, 9 July 2013.



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