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<p><b>Abstract</b>—We present C<scp>ompu</scp>C<scp>ell</scp>3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. C<scp>ompu</scp>C<scp>ell</scp>3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. C<scp>ompu</scp>C<scp>ell</scp>3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified C<scp>ompu</scp>C<scp>ell</scp>3D 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 <url></url>.</p>
Cellular Potts Model (CPM), biological development, reaction-diffusion, cellular automata, morphogenesis, Extensible Markup Language (XML).

J. A. Izaguirre et al., "A Framework for Three-Dimensional Simulation of Morphogenesis," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. , pp. 273-288, 2005.
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