geometries

!!!! DISCLAIMER !!!!

The summary of tools that support spatial modeling/geometries is a preliminary effort and may not be complete/accurate. If anyone has more information or a better understanding of how the spatial/geometry representations work in any of all of the tools presented, please feel free to edit it with the correct information!

!!!! END DISCLAIMER !!!!

VCell

• 1-d, 2-d, 3-d geometries possible.
• Geometry:
  • Analytic (specify origin, extent, analytic expn for shape)
  • Image-based (construct from segmented image)
• Boundary conditions: Dirichlet, Neumann, Periodic
• Membrane diffusion

MesoRD

• Reaction-Diffusion simulator in 3D space
• Reaction volume is discretized into a large number of small subvolumes (currently only a cube). State of the system is given by the number of molecules per subvolume
• Uses SBML to define geometry (annotations added to <compartment>. Every compartment needs a geometry. All compartments are 3D; size ignored)
• Periodic boundary condn. - for boxes (in x,y,z) and cylinders (y only)

JSim

• Supports only 1st degree PDEs in 1-d (no question of geometry). Specify length; # of spatial grid points
• BCs: Dirichlet, Neumann, Total Flux
• Diffusion and advection possible

SmartCell

• Geometry defined with voxels(?)
• Pre-defined geometry: created from tomogram images
• User-defined geometry: specify shape (cube, sphere, ellipsoid); dimension; # of voxels in x,y,z; voxel size
• For compartments specify 'has Membrane' or 'has Boundary'...
• Supports membrane diffusion (how?)

MCell

• Simulation events occur on OR around surface of physical object
• Possible 'geometries' or 'physical objects': ligand release site, box object, polygon list object
  • Ligand release site: spherical. Specify location, diameter, etc.
  • Box object: cube/cuboids (by default, each face perpendicular to one of x,y,z axes). Specify LLF and URB points; closed or open; surface modifiers (permeability, removing surface, tiling surface with stationary molecule, adding active zones to physical objects, color to surface elements)
  • Polygon list object: obtained from 3d reconstruction, objects designed by graphics tools or defined as physical objects. Each surface element - a planar polygon
  • Meta object: aggregation of physical objects
• Surface regions are defined on object templates (different from surface elements?)
• Surface permeability (of physical objects) to molecules: transparent, absorptive, reflective
• Possible geometric transformations on any 'physical object' : translate, rotate, scale
• Units: um
• Appears to have only 3-d physical objects,
• Surfaces are 2-d?
• Diffusion/Transport of molecules - Brownian motion

ChemCell

• Geometry: simple 3-d primitives (spheres, boxes) or 2-d triangulated surfaces
• Cannot create cellular geometries
• Diffusion : Brownian motion. Particles diffuse within specified geometry (3d or 2d) of cell
• Diffusing entity (protein, complex, biomolecule) - dimensionless particle
• The triangles and region commands are used to create geometric objects and membrane boundaries

Smoldyn

• Membranes modeled by surfaces that
  • Are comprised of many 'panels' (for 3-d, panels can be rectangles, triangles, spheres, etc) [panels subvolumes/regions?]
  • Have rules that specify molecular interaction with surface (surface-bound, diffused); all panels in one surface follow same rules

GridCell

• 3-D stochastic environment
• Simulation space divided into 3-D cubic grid of discrete voxels (voxel size specified as input in m^3)
• System described in SBML
• 3-D structure of particles specified by 'structure file'
  • Specifies shape & size of simulation space (always a cuboidal space?)
  • Specifies species initial location and quantity
  • If not specified, particles randomly placed in 3-D volume

StochSim

• 2-d spatial structures (to simulate nearest-neighbor interactions of molecules)
• Possible geometries: Square, triangles, hexagon (molecules at nodes (corners) of geometry)
  • Real or toroidal boundaries??

CompuCell3D

• 3-D geometry
• Though there is a 2-d example (?)
• Appears to be a lattice model, where the lattice itself is the geometry

E-Cell

• E-Cell Version 4 plans generic representation of space:
  • Support for particle, lattice, and compartment space representations
  • Mixed uses of different spatial representations in a model