CompuCell3D (CC3D) runs 3D multiscale multi-cell simulations, integrating the GGH model , PDE solvers (reaction-diffusion), and cell type automata (differentiation). CompuCell3D runs in parallel with the CompuCellPlayer visualization engine.
CompuCell3D was originally written to model morphogenesis, the process in embryonic development where cells cluster into patterns which eventually differentiate into organs, muscle or bone. Through integration of multiple mathematical models into a software implementation with easy to use XML based syntax scientists were able to build models within few hours as opposed to weeks when writing source code from scratch. compuCell3D is based on Glazier-graner-Hogeweg model (GGH) also known as the Cellular Potts Model (CPM).The model is capable of capturing key cellular behaviors: cell clustering as well as growth, division, death, intracellular adhesion, and volume and surface area constraints;
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Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier
A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation
PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002155