A framework for three-dimensional simulation of morphogenesis.

Trevor M Cickovski; Chenbang Huang; Rajiv Chaturvedi; Tilmann Glimm; H George E Hentschel; Mark S Alber; James A Glazier; Stuart A Newman; Jesús A Izaguirre

doi:10.1109/tcbb.2005.46

PubMed · 17044166

A framework for three-dimensional simulation of morphogenesis.

Trevor M Cickovski·Chenbang Huang·Rajiv Chaturvedi·Tilmann Glimm·H George E Hentschel·Mark S Alber·James A Glazier·Stuart A Newman·Jesús A Izaguirre

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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 http:// compucell.sourceforge.net.

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Animals Cell Physiological Phenomena Chick Embryo Chickens Chondrogenesis Computer Simulation Computing Methodologies Database Management Systems Energy Metabolism Forelimb Models, Biological Morphogenesis Programming Languages User-Computer Interface Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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Trevor M Cickovski, Chenbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H George E Hentschel, Mark S Alber, James A Glazier, Stuart A Newman, Jesús A Izaguirre. A framework for three-dimensional simulation of morphogenesis.. https://doi.org/10.1109/tcbb.2005.46

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