Herajy Mostafa, Liu Fei, Heiner Monika
Faculty of Science, Port Said University, Department of Mathematics and Computer Science, Port Said, 42521, Port Said, Egypt.
School of Software Engineering, South China University of Technology, Guangzhou, 510006, Guangzhou, China.
Biosystems. 2025 Jan;247:105365. doi: 10.1016/j.biosystems.2024.105365. Epub 2024 Nov 22.
With the steady advance of in-silico biological experimentation, model construction and simulation becomes a ubiquitous tool to understand and predict the behaviour of many biological systems. However, biological processes may contain components from different types of reaction networks, resulting in models with different (e.g., slow and fast) timescales. Hybrid simulation is one approach which can be employed to efficiently execute multi-timescale models. In this paper, we present a methodology and workflow utilizing (coloured) hybrid Petri nets to construct smaller and more complicated hybrid models. The presented workflow integrates algorithms and ideas from hybrid simulation of biochemical reaction networks as well as Petri nets. We also construct multi-timescale hybrid models and then show how these models can be efficiently executed using three different advanced hybrid simulation algorithms.
随着计算机模拟生物学实验的稳步推进，模型构建和模拟成为理解和预测许多生物系统行为的普遍工具。然而，生物过程可能包含来自不同类型反应网络的组件，从而导致模型具有不同（例如，慢和快）的时间尺度。混合模拟是一种可用于高效执行多时间尺度模型的方法。在本文中，我们提出了一种利用（有色）混合Petri网构建更小且更复杂混合模型的方法和工作流程。所提出的工作流程整合了来自生化反应网络混合模拟以及Petri网的算法和思想。我们还构建了多时间尺度混合模型，然后展示如何使用三种不同的先进混合模拟算法来高效执行这些模型。
