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ABSTRACT
<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>http://compucell.sourceforge.net</url>.</p>
INDEX TERMS
Cellular Potts Model (CPM), biological development, reaction-diffusion, cellular automata, morphogenesis, Extensible Markup Language (XML).
CITATION
Jes?s A. Izaguirre, James A. Glazier, H. George E. Hentschel, Rajiv Chaturvedi, Trevor M. Cickovski, Stuart A. Newman, Tilmann Glimm, Chengbang Huang, Mark S. Alber, "A Framework for Three-Dimensional Simulation of Morphogenesis", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. , pp. 273-288, October-December 2005, doi:10.1109/TCBB.2005.46
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