Sego T J, Comlekoglu Tien, Peirce Shayn M, Desimone Douglas, Glazier James A
Department of Medicine, University of Florida, Gainesville, FL, USA.
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Res Sq. 2023 May 8:rs.3.rs-2886960. doi: 10.21203/rs.3.rs-2886960/v1.
Vertex models are a widespread approach for describing the biophysics and behaviors of multicellular systems, especially of epithelial tissues. Vertex models describe a wide variety of developmental scenarios and behaviors like cell rearrangement and tissue folding. Often, these models are implemented as single-use or closed-source software, which inhibits reproducibility and decreases accessibility for researchers with limited proficiency in software development and numerical methods. We developed a physics-based vertex model methodology in Tissue Forge, an open-source, particle-based modeling and simulation environment. Our methodology describes the properties and processes of vertex model objects on the basis of vertices, which allows integration of vertex modeling with the particle-based formalism of Tissue Forge, enabling an environment for developing mixed-method models of multicellular systems. Our methodology in Tissue Forge inherits all features provided by Tissue Forge, delivering opensource, extensible vertex modeling with interactive simulation, real-time simulation visualization and model sharing in the and Python programming languages and a Jupyter Notebook. Demonstrations show a vertex model of cell sorting and a mixed-method model of cell migration combining vertex- and particle-based models. Our methodology provides accessible vertex modeling for a broad range of scientific disciplines, and we welcome community-developed contributions to our open-source software implementation.
顶点模型是一种广泛用于描述多细胞系统，尤其是上皮组织的生物物理学和行为的方法。顶点模型描述了各种各样的发育场景和行为，如细胞重排和组织折叠。通常，这些模型是作为一次性使用或闭源软件实现的，这抑制了可重复性，并降低了软件开发和数值方法熟练程度有限的研究人员的可及性。我们在Tissue Forge中开发了一种基于物理的顶点模型方法，Tissue Forge是一个开源的、基于粒子的建模和模拟环境。我们的方法基于顶点描述顶点模型对象的属性和过程，这使得顶点建模能够与Tissue Forge基于粒子的形式主义相结合，从而为开发多细胞系统的混合方法模型提供了一个环境。我们在Tissue Forge中的方法继承了Tissue Forge提供的所有功能，提供了开源的、可扩展的顶点建模，具有交互式模拟、实时模拟可视化以及使用C++和Python编程语言以及Jupyter Notebook进行模型共享。演示展示了细胞分选的顶点模型以及结合了基于顶点和基于粒子模型的细胞迁移混合方法模型。我们的方法为广泛的科学学科提供了可及的顶点建模，并且我们欢迎社区为我们的开源软件实现做出贡献。
