CompuCell, a multi-model framework for simulation of morphogenesis
CompuCell, a multi-model framework for simulation of morphogenesis
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DOI：
10.1093/bioinformatics/bth050
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发表时间：
2004-05-01
期刊：
影响因子：
5.8
通讯作者：
Glazier, JA
中科院分区：
文献类型：
--
作者：
Izaguirre, JA;Chaturvedi, R;Glazier, JA
动机：CompuCell是一个多模型软件框架，用于模拟被称为形态发生的多细胞生物的发育。它模拟了基因调控网络与一般细胞机制的相互作用，如细胞粘附、分裂、趋近性和趋化性。结合随机局部规则的状态自动机和一组微分方程，包括亚细胞常微分方程和细胞外反应扩散偏微分方程，模型基因调控。这种自动机反过来控制细胞的分化，以及细胞间和细胞外基质的相互作用，从而引起细胞重排和模式形成，例如间充质凝聚。细胞波茨模型是一种精确再现细胞运动和重排的随机模型，它模拟了细胞动力学。所有这些模型以一种可控的方式耦合在一起，形成了一个强大而灵活的形态发生计算环境，它允许同时结合生长和空间模式。结果：用计算机模拟了鸟类肢芽骨骼结构的形成过程。
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.