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Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser
The cellular Potts model (CPM) is a powerful in silico method for simulating biological processes at tissue scale. Their inherently graphical nature makes CPMs very accessible in theory, but in practice, they are mostly implemented in specialised frameworks users need to master before they can run s...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143789/ https://www.ncbi.nlm.nih.gov/pubmed/33835022 http://dx.doi.org/10.7554/eLife.61288 |
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author | Wortel, Inge MN Textor, Johannes |
author_facet | Wortel, Inge MN Textor, Johannes |
author_sort | Wortel, Inge MN |
collection | PubMed |
description | The cellular Potts model (CPM) is a powerful in silico method for simulating biological processes at tissue scale. Their inherently graphical nature makes CPMs very accessible in theory, but in practice, they are mostly implemented in specialised frameworks users need to master before they can run simulations. We here present Artistoo (Artificial Tissue Toolbox), a JavaScript library for building ‘explorable’ CPM simulations where viewers can change parameters interactively, exploring their effects in real time. Simulations run directly in the web browser and do not require third-party software, plugins, or back-end servers. The JavaScript implementation imposes no major performance loss compared to frameworks written in C++; Artistoo remains sufficiently fast for interactive, real-time simulations. Artistoo provides an opportunity to unlock CPM models for a broader audience: interactive simulations can be shared via a URL in a zero-install setting. We discuss applications in CPM research, science dissemination, open science, and education. |
format | Online Article Text |
id | pubmed-8143789 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-81437892021-05-26 Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser Wortel, Inge MN Textor, Johannes eLife Cell Biology The cellular Potts model (CPM) is a powerful in silico method for simulating biological processes at tissue scale. Their inherently graphical nature makes CPMs very accessible in theory, but in practice, they are mostly implemented in specialised frameworks users need to master before they can run simulations. We here present Artistoo (Artificial Tissue Toolbox), a JavaScript library for building ‘explorable’ CPM simulations where viewers can change parameters interactively, exploring their effects in real time. Simulations run directly in the web browser and do not require third-party software, plugins, or back-end servers. The JavaScript implementation imposes no major performance loss compared to frameworks written in C++; Artistoo remains sufficiently fast for interactive, real-time simulations. Artistoo provides an opportunity to unlock CPM models for a broader audience: interactive simulations can be shared via a URL in a zero-install setting. We discuss applications in CPM research, science dissemination, open science, and education. eLife Sciences Publications, Ltd 2021-04-09 /pmc/articles/PMC8143789/ /pubmed/33835022 http://dx.doi.org/10.7554/eLife.61288 Text en © 2021, Wortel and Textor https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Cell Biology Wortel, Inge MN Textor, Johannes Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
title | Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
title_full | Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
title_fullStr | Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
title_full_unstemmed | Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
title_short | Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
title_sort | artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser |
topic | Cell Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143789/ https://www.ncbi.nlm.nih.gov/pubmed/33835022 http://dx.doi.org/10.7554/eLife.61288 |
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