{"id":107440,"date":"2024-09-23T16:39:15","date_gmt":"2024-09-23T20:39:15","guid":{"rendered":"https:\/\/med.virginia.edu\/cell-biology\/?p=107440"},"modified":"2025-05-15T11:38:24","modified_gmt":"2025-05-15T15:38:24","slug":"general-open-source-vertex-modeling-in-biological-applications-using-tissue-forge","status":"publish","type":"post","link":"https:\/\/med.virginia.edu\/cell-biology\/2024\/09\/23\/general-open-source-vertex-modeling-in-biological-applications-using-tissue-forge\/","title":{"rendered":"General, open-source vertex modeling in biological applications using Tissue Forge"},"content":{"rendered":"

UVA Author:<\/strong> Tien Comlekoglu
\nCitation:<\/strong> Sego TJ, Comlekoglu T, Peirce SM, Desimone DW, Glazier JA. General, open-source vertex modeling in biological applications using Tissue Forge. Sci Rep. 2023 Oct 19;13(1):17886. doi: 10.1038\/s41598-023-45127-x. PMID: 37857673; PMCID: PMC10587242.<\/p>\n

DOI:<\/strong> https:\/\/doi.org\/10.1038\/s41598-023-45127-x<\/a>
\nPub-Med Number<\/strong>: 37857673<\/p>\n

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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.<\/p>\n<\/div>\n<\/div>\n<\/section>\n","protected":false},"excerpt":{"rendered":"

UVA Author: Tien Comlekoglu Citation: Sego TJ, Comlekoglu T, Peirce SM, Desimone DW, Glazier JA. General, open-source vertex modeling in biological applications using Tissue Forge. Sci Rep. 2023 Oct 19;13(1):17886. doi: 10.1038\/s41598-023-45127-x. PMID: 37857673; PMCID: PMC10587242. DOI: https:\/\/doi.org\/10.1038\/s41598-023-45127-x Pub-Med Number: 37857673 Vertex models are a widespread approach for describing the biophysics and behaviors of multicellular […]<\/p>\n","protected":false},"author":1740,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[13],"tags":[],"class_list":["post-107440","post","type-post","status-publish","format-standard","hentry","category-featured-publications"],"acf":false,"yoast_head":"\nGeneral, open-source vertex modeling in biological applications using Tissue Forge - Department of Cell Biology<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/med.virginia.edu\/cell-biology\/2024\/09\/23\/general-open-source-vertex-modeling-in-biological-applications-using-tissue-forge\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"General, open-source vertex modeling in biological applications using Tissue Forge - Department of Cell Biology\" \/>\n<meta property=\"og:description\" content=\"UVA Author: Tien Comlekoglu Citation: Sego TJ, Comlekoglu T, Peirce SM, Desimone DW, Glazier JA. 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