Tanaka Simon, Sichau David, Iber Dagmar
Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and Swiss Institute of Bioinformatics, Basel, Switzerland.
Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and.
Bioinformatics. 2015 Jul 15;31(14):2340-7. doi: 10.1093/bioinformatics/btv147. Epub 2015 Mar 13.
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell-cell interactions and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required.
We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics.
The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html
形态发生问题的模拟需要同时对信号传导和组织动力学进行耦合模拟。对组织域进行细胞分辨率的模拟对于充分描述基于细胞的事件（如细胞分裂、细胞间相互作用和空间受限的信号传导事件）的影响至关重要。因此，需要一个紧密耦合的基于细胞的机械调节模拟工具。
我们开发了一个用于形态发生问题的开源软件框架。该环境为组织和信号模型提供了核心功能。此外，该软件在添加自定义扩展和具有生物学动机的过程方面具有很大的灵活性。细胞被表示为高度解析的无质量弹性多边形；组织的粘性特性由牛顿流体建模。浸入边界方法用于模拟细胞粘性和弹性特性之间的相互作用，从而在IBCell模型的基础上进行了扩展。流体和信号传导过程使用格子玻尔兹曼方法求解。作为应用示例，我们模拟了信号依赖的组织动力学。
文档和源代码可在http://tanakas.bitbucket.org/lbibcell/index.html上获取。
