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

eLife

Inge MN Wortel¹  Johannes Textor¹ 

[1] Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands;Institute for Computing and Information Sciences, Data Science, Radboud University, Nijmegen, Netherlands;

关键词: cellular Potts model;    simulation;    software;    science communication;    tissue-scale model;    None;   

DOI  :  10.7554/eLife.61288

来源: eLife Sciences Publications, Ltd

【 摘 要 】

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.

【 授权许可】

CC BY