Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser.
Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser.
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DOI：
10.7554/elife.61288
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发表时间：
2021-04-09
期刊：
影响因子：
7.7
通讯作者：
Textor J
中科院分区：
文献类型：
--
作者：
Wortel IM;Textor J
细胞Potts模型（CPM）是一种在组织尺度上模拟生物过程的强大的计算机方法。它们固有的图形化特性使得CPM在理论上非常容易使用，但在实践中，它们主要是在用户需要在运行模拟之前掌握的专门框架中实现的。我们在这里提出了Artistoo（人工组织），一个JavaScript库，用于构建“可探索的”CPM模拟，观众可以交互式地更改参数，探索他们的效果在真实的时间。模拟直接在Web浏览器中运行，不需要第三方软件、插件或后端服务器。与用C++编写的框架相比，JavaScript实现不会造成重大性能损失; Artistoo对于交互式实时模拟仍然足够快。Artistoo为更广泛的受众提供了解锁CPM模型的机会：可以通过零安装设置中的URL共享交互式模拟。我们讨论了CPM研究，科学传播，开放科学和教育中的应用。理解复杂的系统，如天气或流行病的传播，通常依赖于可以模拟正在发生的事情和接下来会发生什么的计算模型。像这样的模型也可以用来研究生物过程。例如，细胞Potts模型（或简称CPM）经常用于模拟细胞如何移动，自组织形成组织并对其周围环境做出反应。计算生物学家使用一系列专业技能和软件来创建这些模型。然而，这可能会使没有编程经验的人难以与这些模拟进行交互并将其纳入自己的研究。如果更多的人能够参与这些模型，这将有助于促进更密切的合作，并最终导致更好的生物系统模型。为了使CPM更容易访问，Wortel和Textor创建了一个名为Artistoo的工具箱，允许用户仅使用互联网浏览器查看模拟并与之交互。这些模拟非常容易交互，不需要任何编程知识或专业软件。观众可以在模拟中输入不同的参数，并在真实的时间内观看，看看这如何影响正在建模的生物系统。Wortel和Textor表明，这个工具箱可以用来构建一系列不同的生物模型，并且与其他更复杂的编程工具一样快。Artistoo有许多潜在的应用程序，是一个有价值的教育，学习和协作工具。它还可以鼓励更多的开放科学，因为拥有更容易访问的计算模型可以帮助同行评审，并使不同研究领域的合作更加容易。类似的方法可用于提供对生物学及其他领域许多其他类型模型的访问。
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. 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.