Ruscone Marco, Checcoli Andrea, Heiland Randy, Barillot Emmanuel, Macklin Paul, Calzone Laurence, Noël Vincent
Institut Curie, Université PSL, F-75005, Paris, France.
INSERM, U900, F-75005, Paris, France.
ArXiv. 2024 Jun 26:arXiv:2406.18371v1.
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the intracellular level such as signaling, and at the extracellular level where cells communicate and coordinate with other cells. They aim to understand the impact of genetic or environmental deregulation observed in complex diseases, describe the interplay between a pathological tissue and the immune system, and suggest strategies to revert the diseased phenotypes. The construction of these multiscale models remains a very complex task, including the choice of the components to consider, the level of details of the processes to simulate, or the fitting of the parameters to the data. One additional difficulty is the expert knowledge needed to program these models in languages such as C++ or Python, which may discourage the participation of non-experts. Simplifying this process through structured description formalisms - coupled with a graphical interface - is crucial in making modeling more accessible to the broader scientific community, as well as streamlining the process for advanced users. This article introduces three examples of multiscale models which rely on the framework PhysiBoSS, an add-on of PhysiCell that includes intracellular descriptions as continuous time Boolean models to the agent-based approach. The article demonstrates how to easily construct such models, relying on PhysiCell Studio, the PhysiCell Graphical User Interface. A step-by-step tutorial is provided as a Supplementary Material and all models are provided at: https://physiboss.github.io/tutorial/.
多尺度模型为研究复杂过程提供了一种独特的工具，这些复杂过程涵盖了在空间和时间上不同尺度发生的事件。在生物系统的背景下，此类模型可以模拟细胞内水平发生的机制，如信号传导，以及细胞与其他细胞进行通信和协调的细胞外水平的机制。它们旨在了解在复杂疾病中观察到的基因或环境失调的影响，描述病理组织与免疫系统之间的相互作用，并提出恢复疾病表型的策略。构建这些多尺度模型仍然是一项非常复杂的任务，包括要考虑的组件的选择、要模拟的过程的细节程度，或参数与数据的拟合。另一个困难是需要用C++ 或Python等语言对这些模型进行编程的专业知识，这可能会阻碍非专业人员的参与。通过结构化描述形式主义（结合图形界面）简化这一过程，对于使更广泛的科学界更容易进行建模以及简化高级用户的流程至关重要。本文介绍了三个多尺度模型的示例，这些模型依赖于PhysiBoSS框架，PhysiBoSS是PhysiCell的一个附加组件，它将细胞内描述作为连续时间布尔模型纳入基于代理的方法。本文展示了如何依靠PhysiCell Studio（PhysiCell图形用户界面）轻松构建此类模型。作为补充材料提供了一个分步教程，所有模型可在以下网址获取：https://physiboss.github.io/tutorial/ 。
