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A Framework for Three-Dimensional Simulation of Morphogenesis
October-December 2005 (vol. 2 no. 4)
pp. 273-288

Abstract—We present CompuCell3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. CompuCell3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. CompuCell3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified CompuCell3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at

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Index Terms:
Cellular Potts Model (CPM), biological development, reaction-diffusion, cellular automata, morphogenesis, Extensible Markup Language (XML).
Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jes?s A. Izaguirre, "A Framework for Three-Dimensional Simulation of Morphogenesis," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 4, pp. 273-288, Oct.-Dec. 2005, doi:10.1109/TCBB.2005.46
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