Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser

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Abstract

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.

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Source scripts have been provided for Figure 2.

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Author details

Inge M N Wortel

Institute for Computing and Information Sciences, Data Science, Radboud University, Nijmegen, Netherlands

For correspondence
inge.wortel@ru.nl

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3362-5229
Johannes Textor

Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands

For correspondence
johannes.textor@ru.nl

Competing interests
The authors declare that no competing interests exist.

Funding

KWF Kankerbestrijding (Young Investigator Grant,10620)

Johannes Textor

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Vidi Grant,192.084)

Johannes Textor

Radboud Universitair Medisch Centrum (Master-PhD grant)

Inge M N Wortel

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.