A framework for three-dimensional simulation of morphogenesis

被引：67

作者：

Cickovski, TM

Huang, CB

Chaturvedi, R

Glimm, T

Hentschel, HGE

Alber, MS

Glazier, JA

Newman, SA

Izaguirre, JA

机构：

[1] Univ Notre Dame, Dept Comp Sci & Engn, Lab Computat Life Sci, Notre Dame, IN 46556 USA

[2] Emory Univ, Dept Phys, Atlanta, GA 30322 USA

[3] Univ Notre Dame, Dept Math, Notre Dame, IN 46556 USA

[4] Indiana Univ, Dept Phys, Bloomington, IN 47405 USA

[5] New York Med Coll, Valhalla, NY 10595 USA

来源：

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | 2005年 / 2卷 / 04期

基金：

美国国家科学基金会; 美国国家航空航天局;

关键词：

Cellular Potts Model (CPM); biological development; reaction-diffusion; cellular automata; morphogenesis; Extensible Markup Language (XML);

D O I：

10.1109/TCBB.2005.46

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：273 / 288

页数：16

共 94 条

[1] Stability of n-dimensional patterns in a generalized Turing system:: implications for biological pattern formation [J].