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bioRxiv · 10.1101/2020.05.01.072975

Artistoo: build, share, and explore simulations of cells and tissues in the web browser

Wortel, I. M. N.·Textor, J.
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Abstract

SummaryThe Cellular Potts Model (CPM) is a powerful in silico method for simulating diverse biological processes at tissue scale. Because of its inherently graphical nature, this model should in theory be accessible to a large audience of biologists - without requiring extensive mathematical expertise. But in practice, CPMs are mostly implemented in specialized frameworks that users need to master before they can run and modify the simulation. We here present Artistoo (Artificial Tissue Toolbox), a JavaScript library for building "explorable" CPM simulations where users can change model parameters and see their effects in real time. Artistoo simulations run directly in the web browser and do not require any third-party software, plugins, or back-end servers. Although implemented in JavaScript, Artistoo does not suffer from a major performance loss compared to frameworks written in C++; it remains sufficiently fast to let users interact with simulations in real time. Artistoo provides an opportunity to unlock CPM models for a broader audience: interactive simulations can be shared through a simple URL in a zero-install setting. We discuss how such model sharing may benefit modelling research, science dissemination, open science, and education. Availability and ImplementationArtistoo is an open-source library released under the MIT license, and is freely available on GitHub at https://github.com/ingewortel/artistoo. ContactJohannes.Textor@radboudumc.nl

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Wortel, I. M. N., Textor, J.. 2020-05-03. Artistoo: build, share, and explore simulations of cells and tissues in the web browser. https://doi.org/10.1101/2020.05.01.072975

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