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Literature DB >> 17044166

A framework for three-dimensional simulation of morphogenesis.

Trevor M Cickovski¹, Chenbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H George E Hentschel, Mark S Alber, James A Glazier, Stuart A Newman, Jesús A Izaguirre.

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.

Entities: Species

Mesh：

Year: 2005 PMID： 17044166 DOI： 10.1109/TCBB.2005.46

Source DB: PubMed Journal: IEEE/ACM Trans Comput Biol Bioinform ISSN： 1545-5963 Impact factor: 3.710

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Cited

24 in total

1. On multiscale approaches to three-dimensional modelling of morphogenesis.

Authors: R Chaturvedi; C Huang; B Kazmierczak; T Schneider; J A Izaguirre; T Glimm; H G E Hentschel; J A Glazier; S A Newman; M S Alber
Journal: J R Soc Interface Date: 2005-06-22 Impact factor: 4.118

2. A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.

Authors: Nan Chen; James A Glazier; Jesús A Izaguirre; Mark S Alber
Journal: Comput Phys Commun Date: 2007-06 Impact factor: 4.390

3. Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb.

Authors: Nikodem J Popławski; Maciej Swat; J Scott Gens; James A Glazier
Journal: Physica A Date: 2007-01-01 Impact factor: 3.263

4. Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment.

Authors: Nikodem J Popławski; Abbas Shirinifard; Maciej Swat; James A Glazier
Journal: Math Biosci Eng Date: 2008-04 Impact factor: 2.080

A framework for three-dimensional simulation of morphogenesis.

1. On multiscale approaches to three-dimensional modelling of morphogenesis.

2. A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.

3. Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb.

4. Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment.

5. Individual-based and continuum models of growing cell populations: a comparison.

6. From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development.

7. Front instabilities and invasiveness of simulated avascular tumors.

8. Computational modeling of epithelial-mesenchymal transformations.

9. A mathematical model to study the dynamics of epithelial cellular networks.

10. Growth based morphogenesis of vertebrate limb bud.