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

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 Understanding complex systems, such as the weather or the spread of a pandemic, often relies on computational models that can simulate what is happening and what will happen next. Models like these can also be used to investigate biological processes. For example, cellular Potts models (or CPMs for short) are regularly used to simulate how cells move, self-organise to form tissues and respond to their surroundings. Computational biologists use a range of specialist skills and software to create these models. However, this can make it difficult for people who do not have programming experience to interact with these simulations and incorporate them in to their own research. If more people could engage with these models, this could help foster closer collaborations and ultimately lead to better models of biological systems. To make CPMs more accessible, Wortel and Textor created a toolbox called Artistoo that allows users to view and interact with simulations using just an internet browser. These simulations are very easy to interact with, and do not require any prior programming knowledge or specialised software. Viewers can input different parameters in to the simulation and watch in real time to see how this affects the biological system being modelled. Wortel and Textor showed that this toolbox can be used to build a range of different biological models and works just as fast as other, more complex programming tools. Artistoo has many potential applications and is a valuable education, learning, and collaboration tool. It may also encourage more open science, as having more accessible computational models could help with peer review and make it easier to collaborate across different research fields. A similar approach could be used to provide access to many other types of models in biology and beyond.

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© 2021, Wortel and Textor.

Déclaration de conflit d'intérêts

IW, JT No competing interests declared