General, open-source vertex modeling in biological applications using Tissue Forge
Abstract 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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-45127-x |
| _version_ | 1797453163821793280 |
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| author | T. J. Sego Tien Comlekoglu Shayn M. Peirce Douglas W. Desimone James A. Glazier |
| author_facet | T. J. Sego Tien Comlekoglu Shayn M. Peirce Douglas W. Desimone James A. Glazier |
| author_sort | T. J. Sego |
| collection | DOAJ |
| description | Abstract 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 open-source, extensible vertex modeling with interactive simulation, real-time simulation visualization and model sharing in the C, C++ 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. |
| first_indexed | 2024-03-09T15:18:53Z |
| format | Article |
| id | doaj.art-cca8aa6c5fa04ead9d2aafdc8fad9691 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:18:53Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-cca8aa6c5fa04ead9d2aafdc8fad96912023-11-26T12:55:44ZengNature PortfolioScientific Reports2045-23222023-10-0113111710.1038/s41598-023-45127-xGeneral, open-source vertex modeling in biological applications using Tissue ForgeT. J. Sego0Tien Comlekoglu1Shayn M. Peirce2Douglas W. Desimone3James A. Glazier4Department of Medicine, University of FloridaDepartment of Biomedical Engineering, University of VirginiaDepartment of Biomedical Engineering, University of VirginiaDepartment of Cell Biology, University of VirginiaDepartment of Intelligent Engineering and Biocomplexity Institute, Indiana UniversityAbstract 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 open-source, extensible vertex modeling with interactive simulation, real-time simulation visualization and model sharing in the C, C++ 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.https://doi.org/10.1038/s41598-023-45127-x |
| spellingShingle | T. J. Sego Tien Comlekoglu Shayn M. Peirce Douglas W. Desimone James A. Glazier General, open-source vertex modeling in biological applications using Tissue Forge Scientific Reports |
| title | General, open-source vertex modeling in biological applications using Tissue Forge |
| title_full | General, open-source vertex modeling in biological applications using Tissue Forge |
| title_fullStr | General, open-source vertex modeling in biological applications using Tissue Forge |
| title_full_unstemmed | General, open-source vertex modeling in biological applications using Tissue Forge |
| title_short | General, open-source vertex modeling in biological applications using Tissue Forge |
| title_sort | general open source vertex modeling in biological applications using tissue forge |
| url | https://doi.org/10.1038/s41598-023-45127-x |
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