Geometry

SBML Level 3 Package Activity Status 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. SBML models today are nonspatial: compartments are topological structures only, with dimensionality, size and containment being their only physical attributes. This was partly a conscious design decision, because there are far more nonspatial modeling tools available today 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 geom.

Active 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 Geometry in SBML Level 3:

Although there are no active proposals at this time, there is an activity page for the SBML Level 3 Geometry effort.

Active specifications

There are no active specifications for the SBML Level 3 Geometry package at this time.