TABLE I.
A comparison of frameworks for biological modeling and simulation that include modeling of the cellular level. It should be noted that newer versions of the surveyed software may contain features that are not mentioned in this table.
| Name of systems | Biological scale | Paradigm | Medium | Visualization capabilities | Real-time interactivity | Features for scalability |
|---|---|---|---|---|---|---|
| MSI28 | Multiscale-cellular and intracellular | Agent-based | Yes | Non-real-time 3D | None | Parallelization |
| EPISIM29,30 | Multiscale-cellular and intracellular using COPASI | Multi paradigm | No | Real-time 2D and 3D | Simulation parameter control | Parallelization |
| LINDSAY31 | Cellular | Agent-based | No | Real-time 3D visualization | Moving camera, simulation parameter control | Distributed computing |
| SimuLife32 | Cellular | “Reactive animation” | Yes | Real-time 3D | Moving camera, simulation parameter control | Client–server architecture on web |
| FLAME-GPU33–35 | Cellular, subcellular if linked to COPASI | Agent-based | No, but can be linked to other simulators to enable a medium | 3D visualization | In later versions | GPU used for non-graphical tasks |
| Simmune36,37 | Multiscale | Multi-paradigm–agent based, 3D grid | Yes | Non-graphical output of data | No | No |
| C-ImmSim38 | Multiscale–cellular and intracellular | Agent-based | Yes | Non-graphical output of data | No | No, but following system “ImmunoGrid” uses grid technologies for scalability45 |
| CellSys39 | Cellular | Agent-based | Yes | Real-time 3D with medium field visualization | No | Parallelization using OpenMP |
| Compucell3D40 | Cellular | Cellular Potts model (CPM) or lattice-based Glazier–Graner–Hogeweg (GGH) | Yes | Real-time 3D | No | Parallelization using OpenMP |