Multicellular Frameworks
NOTE: Cellular Potts Model (CPM) is also known as the Glazier-Graner-Hogeweg (GGH) model.
| Name | Model Type | Description | Website |
|---|---|---|---|
| Artistoo | CPM/GGH | A framework for Cellular Potts Models that lets you build interactive, explorable simulation models of cells and tissues in the web browser using Javascript. | link |
| BioDynaMo | Center Model | Software platform to easily create, run, and visualise 3D agent-based simulations | link |
| CompuCell3D | CPM/GGH | A flexible and extensible simulation environment for multi-cellular systems biology, including the use of cellular Potts models. | link |
| Chaste | Multi-Method: CPM/GGH, Center Model, Vertex Model, FE | Chaste (Cancer, Heart and Soft Tissue Environment) is a general-purpose simulation package aimed at simulating biological systems, particularly focusing on cardiac, cancer, and soft tissue modeling. | link |
| Hybrid Automata Library (HAL) | Multi-Method | A Java library that facilitates hybrid modeling: spatial models with interacting agent-based and PDE components, commonly used for oncology modeling. | link |
| Morpheus | CPM/GGH | A modeling and simulation environment for the study of multi-scale and multicellular systems, able to couple ODEs, PDEs and cellular Potts models. | link |
| NetLogo | CPM/GGH | A multi-agent programmable modeling environment. | link |
| PhysiCell | Center Model | A physics-based cell simulator that models 3D multicellular systems, focusing on the interactions of (off-lattice) cells with their microenvironment. | link |
| PolyHoop | Vertex Model | A lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. | link |
| SimuCell3D | Center Model | A C++ cell-based simulation framework designed to simulate tissues in 3 dimensions with high geometrical resolution. | link |
| Tissue Forge | Center Model, Vertex Model | Tissue Forge is an interactive, particle-based physics, chemistry and biology modeling and simulation environment. | link |
| Tissue Simulation Toolkit | CPM/GGH | Tissue Simulation Toolkit (TST) 2.0, a library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993). | link |
| Vivarium Collective | Multi Model Integration | The Vivarium Collective is a registry for open-source Vivarium-compatible simulation modules. These can be wired together to generate novel multi-scale simulations, with the most appropriate algorithm for each biological mechanism. | link |