1,2,3 dimensional description of shape and location of membrane bound cellular structures, filaments, points.
- explicit surfaces (polygonal tesselations), identify volumes by adjacency and interior points.
- implicit surfaces, identify surfaces by isosurfaces (e.g. f(x,y,z) == 0).
- volume sampled distance maps (e.g. level sets).
- inside-outside functions (e.g. R-Functions, f(x,y,z)<0).
- geometric primatives (e.g. spheres) with constructive solid geometry (i.e. union, intersection, difference).
- nonuniform continuous field of molecular concentration.
- discrete molecular locations
biological process localization
- no localization, possible when operating on well-stirred pools (current SBML)
- compartmental localization, mapped uniformly to geometric domains associated with a compartment.
- sub-domain localization through spatially varying kinetic parameters
compartmental dimension and domain dimension.