Izaguirre J A, Chaturvedi R, Huang C, Cickovski T, Coffland J, Thomas G, Forgacs G, Alber M, Hentschel G, Newman S A, Glazier J A
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
Bioinformatics. 2004 May 1;20(7):1129-37. doi: 10.1093/bioinformatics/bth050. Epub 2004 Feb 5.
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.
We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud.
Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/
CompuCell是一个多模型软件框架，用于模拟多细胞生物的发育过程，即形态发生。它对基因调控网络与一般细胞机制（如细胞黏附、分裂、趋触性和趋化性）之间的相互作用进行建模。状态自动机与随机局部规则以及一组微分方程（包括亚细胞常微分方程和细胞外反应扩散偏微分方程）相结合，对基因调控进行建模。这个自动机进而控制细胞的分化以及细胞间和细胞与细胞外基质的相互作用，这些相互作用会导致细胞重排和模式形成，例如间充质凝聚。细胞Potts模型是一种能准确再现细胞运动和重排的随机模型，用于对细胞动力学进行建模。所有这些模型以可控的方式耦合在一起，形成了一个用于形态发生的强大且灵活的计算环境，该环境允许同时纳入生长和空间模式形成。
我们使用CompuCell来模拟鸟类肢体芽中骨骼结构的形成。
适用于Microsoft Windows、Linux和Solaris的二进制文件和源代码可从http://sourceforge.net/projects/compucell/下载
