Advertisement
Table 3 A comparison of features of RDME simulation software
| URDME 1.1 | MesoRD 1.0 | STEPS 1.3 | |
|---|---|---|---|
| Interface | Matlab & Comsol | Command line | Python |
| Simple GUI (Windows) | |||
| Visualization | Matlab & Comsol | OpenGL tool | PyOpenGL tool |
| Matlab toolbox | |||
| Post-processing | Matlab | 3rd party | Python |
| SBML support | Conversion tool | SBML L2v4 | Import module |
| (no geometry) | + CSG geometry | (no geometry) | |
| Edit Geometry | Comsol | SBML | 3rd party |
| Mesh Type | Vertex centered | Uniform Cartesian | Body centered |
| Tetrahedrons | Tetrahedrons | ||
| Algorithms | NSM, DFSP | NSM | Spatial-SSA |
| + extendable | +non-local extension | ||
| Propensity types | All | SBML (MathML) | Mass-action |
| Model Features | compartments | compartments | compartments |
| surfaces | surfaces | ||
| volume diffusion | volume diffusion | volume diffusion | |
| surface diffusion | |||
| directed transport |
