A framework for three-dimensional simulation of morphogenesis

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 2; no. 4; pp. 273 - 288
• Main Authors: Cickovski, T.M., Chengbang Huang, Chaturvedi, R., Glimm, T., Hentschel, H.G.E., Alber, M.S., Glazier, J.A., Newman, S.A., Izaguirre, J.A.
• Format: Journal Article
• Language: English
• Published: United States IEEE 01-10-2005; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Animals; biological development; Biological information theory; Biological system modeling; Biology computing; Cell Physiological Phenomena; Cells (biology); cellular automata; Cellular Potts Model (CPM); Chemicals; Chick Embryo; Chickens; Chondrogenesis; Computational modeling; Computer Simulation; Computing Methodologies; Database Management Systems; Energy Metabolism; Extensible Markup Language (XML); Forelimb - cytology; Forelimb - embryology; Forelimb - physiology; Mathematical model; Models, Biological; Morphogenesis; Organisms; Programming Languages; reaction-diffusion; Shape; User-Computer Interface; XML
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2005.46

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.