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

  1. Inge M N Wortel  Is a corresponding author
  2. Johannes Textor  Is a corresponding author
  1. Radboud University, Netherlands
  2. Radboud Institute for Molecular Life Sciences, Netherlands

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.

Data availability

Source scripts have been provided for Figure 2.

Article and author information

Author details

  1. 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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3362-5229
  2. 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.

Reviewing Editor

  1. Andreas Buttenschoen, University of British Columbia, Canada

Publication history

  1. Received: July 21, 2020
  2. Accepted: April 8, 2021
  3. Accepted Manuscript published: April 9, 2021 (version 1)
  4. Version of Record published: May 24, 2021 (version 2)

Copyright

© 2021, Wortel & Textor

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.

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  1. Inge M N Wortel
  2. Johannes Textor
(2021)
Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser
eLife 10:e61288.
https://doi.org/10.7554/eLife.61288

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