Table 6

Spatial simulators

GridCell

SmartCell

MesoRD

Cell++

MCell

Smoldyn

ChemCell


Molecule representation

Particle

Population

Population

Large particles and populations of small particles

Particle

Particle

Particle

Stochastic

Yes

Yes

Yes

Large particles only

Yes

Yes

Yes

Space

Discretized

Discretized

Discretized

Continuous (large particles) and discretized (small particles)

Continuous

Continuous

Continuous

Particle-collision support

Yes

No

No

No

No

No

No

Diffusion support

Yes

Yes

Yes

Yes

Yes

Yes

Yes

SBML support

Yes

Yes

Yes

No

No

No

No

Web availability

Yes

Yes

Yes

Yes

Yes

Yes

No


Comparison and description of various simulators.

Boulianne et al. BMC Systems Biology 2008 2:66   doi:10.1186/1752-0509-2-66

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