CompuCell, a multi-model framework for simulation of morphogenesis

被引:142
作者
Izaguirre, JA [1 ]
Chaturvedi, R
Huang, C
Cickovski, T
Coffland, J
Thomas, G
Forgacs, G
Alber, M
Hentschel, G
Newman, SA
Glazier, JA
机构
[1] Univ Notre Dame, Dept Comp Sci & Engn, Notre Dame, IN 46556 USA
[2] Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA
[3] Univ Missouri, Dept Phys & Biol, Columbia, MO 65211 USA
[4] Univ Notre Dame, Dept Math, Notre Dame, IN 46556 USA
[5] Emory Univ, Dept Phys, Atlanta, GA 30332 USA
[6] New York Med Coll, Dept Cell Biol & Anat, Valhalla, NY 10595 USA
[7] Indiana Univ, Dept Phys, Bloomington, IN 47405 USA
[8] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
[9] Indiana Univ, Biocomplex Inst, Bloomington, IN 47405 USA
基金
美国国家科学基金会;
关键词
D O I
10.1093/bioinformatics/bth050
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. Results: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud.
引用
收藏
页码:1129 / 1137
页数:9
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