Literature DB >> 33835022

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

Inge M N Wortel1, Johannes Textor2.   

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.
© 2021, Wortel & Textor.

Entities:  

Keywords:  cell biology; computational biology; none; systems biology

Year:  2021        PMID: 33835022     DOI: 10.7554/eLife.61288

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  2 in total

1.  Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics.

Authors:  Leonie van Steijn; Inge M N Wortel; Clément Sire; Loïc Dupré; Guy Theraulaz; Roeland M H Merks
Journal:  PLoS Comput Biol       Date:  2022-02-14       Impact factor: 4.475

2.  Local actin dynamics couple speed and persistence in a cellular Potts model of cell migration.

Authors:  Inge M N Wortel; Ioana Niculescu; P Martijn Kolijn; Nir S Gov; Rob J de Boer; Johannes Textor
Journal:  Biophys J       Date:  2021-05-20       Impact factor: 3.699

  2 in total

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