Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Wortel, Inge MN, Textor, Johannes
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2021
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
_version_ 1783696827267153920
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
work_keys_str_mv AT wortelingemn artistooalibrarytobuildshareandexploresimulationsofcellsandtissuesinthewebbrowser
AT textorjohannes artistooalibrarytobuildshareandexploresimulationsofcellsandtissuesinthewebbrowser