A Framework for Three-Dimensional Simulation of Morphogenesis

作者：Trevor Cickovski, Chengbang Huang, Rajiv R Chaturvedi, Tilmann Glimm, H. G. E. Hentschel, Mark Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre · 发表于：IEEE Transactions on Computational Biology and Bioinformatics · 年份：2005 · DOI：10.1109/tcbb.2005.46 · 被引用次数：129 · 研究领域：Gene Regulatory Network Analysis、Cellular Mechanics and Interactions、Genetics, Aging, and Longevity in Model Organisms

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 http:// compucell.sourceforge.net.