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A cell-centered, agent-based framework that enables flexible environment granularities
BACKGROUND: Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell’s perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736144/ https://www.ncbi.nlm.nih.gov/pubmed/26839017 http://dx.doi.org/10.1186/s12976-016-0030-9 |
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author | Kennedy, Ryan C Ropella, Glen EP Hunt, C Anthony |
author_facet | Kennedy, Ryan C Ropella, Glen EP Hunt, C Anthony |
author_sort | Kennedy, Ryan C |
collection | PubMed |
description | BACKGROUND: Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell’s perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular lattice-based environment. A framework which utilizes a cell’s perspective in an off-lattice environment could improve the overall understanding of biological phenomena. RESULTS: We present an agent-based, discrete event framework, with a demonstrative focus on biomimetic agents. The framework was first developed in 2-dimensions and then extended, with a subset of behaviors, to 3-dimensions. The framework is expected to facilitate studies of more complex biological phenomena through exploitation of a dynamic Delaunay and Voronoi off-lattice environment. We used the framework to model biological cells and to specifically demonstrate basic biological cell behaviors in two- and three-dimensional space. Potential use cases are highlighted, suggesting the utility of the framework in various scenarios. CONCLUSIONS: The framework presented in this manuscript expands on existing cell- and agent-centered methods by offering a new perspective in an off-lattice environment. As the demand for biomimetic models grows, the demand for new methods, such as the presented Delaunay and Voronoi framework, is expected to increase. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12976-016-0030-9) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4736144 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-47361442016-02-03 A cell-centered, agent-based framework that enables flexible environment granularities Kennedy, Ryan C Ropella, Glen EP Hunt, C Anthony Theor Biol Med Model Software BACKGROUND: Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell’s perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular lattice-based environment. A framework which utilizes a cell’s perspective in an off-lattice environment could improve the overall understanding of biological phenomena. RESULTS: We present an agent-based, discrete event framework, with a demonstrative focus on biomimetic agents. The framework was first developed in 2-dimensions and then extended, with a subset of behaviors, to 3-dimensions. The framework is expected to facilitate studies of more complex biological phenomena through exploitation of a dynamic Delaunay and Voronoi off-lattice environment. We used the framework to model biological cells and to specifically demonstrate basic biological cell behaviors in two- and three-dimensional space. Potential use cases are highlighted, suggesting the utility of the framework in various scenarios. CONCLUSIONS: The framework presented in this manuscript expands on existing cell- and agent-centered methods by offering a new perspective in an off-lattice environment. As the demand for biomimetic models grows, the demand for new methods, such as the presented Delaunay and Voronoi framework, is expected to increase. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12976-016-0030-9) contains supplementary material, which is available to authorized users. BioMed Central 2016-02-02 /pmc/articles/PMC4736144/ /pubmed/26839017 http://dx.doi.org/10.1186/s12976-016-0030-9 Text en © Kennedy et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Kennedy, Ryan C Ropella, Glen EP Hunt, C Anthony A cell-centered, agent-based framework that enables flexible environment granularities |
title | A cell-centered, agent-based framework that enables flexible environment granularities |
title_full | A cell-centered, agent-based framework that enables flexible environment granularities |
title_fullStr | A cell-centered, agent-based framework that enables flexible environment granularities |
title_full_unstemmed | A cell-centered, agent-based framework that enables flexible environment granularities |
title_short | A cell-centered, agent-based framework that enables flexible environment granularities |
title_sort | cell-centered, agent-based framework that enables flexible environment granularities |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736144/ https://www.ncbi.nlm.nih.gov/pubmed/26839017 http://dx.doi.org/10.1186/s12976-016-0030-9 |
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