结合DEVS仿真和本体建模对SARS-CoV-2复制进行分层分析

IF 1.3 4区 工程技术 Q4 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS
Ali Ayadi, C. Frydman, Wissame Laddada, I. Imbert, C. Zanni-Merk, L. Soualmia
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引用次数: 0

摘要

本文提出了一个混合分层模型,其中两种建模和仿真方法,离散事件系统规范仿真(DEVS)和语义技术,一起使用,以帮助分析一个主要的医疗保健问题,严重急性呼吸系统综合征-冠状病毒2 (SARS-CoV-2)。事实上,SARS-CoV-2复制过程的复杂性,以及它与细胞成分相互作用的层次尺度范围(从基因组和转录组学扩展到蛋白质组学和代谢组学尺度),以及它们相互交织的复杂方式,使其理解变得非常具有挑战性。因此,通过考虑与受感染细胞的所有相互作用,对复制过程的不同尺度进行建模是至关重要的。结合DEVS模拟和本体论建模的优势,提出了基于分层本体论的SARS-CoV-2病毒复制的微分子(蛋白质组学和代谢组学)和大分子(基因组学和转录组学)DEVS模拟模型。首先,我们展示了将DEVS模拟和语义技术结合在一个通用建模框架中的有用性,以面对不同规模的SARS-CoV-2病毒复制的复杂性。其次,在不同水平上对SARS-CoV-2复制过程进行建模和模拟,为病毒生命周期的不同阶段提供了有价值的信息,并为预测病毒选择的未来突变的系统奠定了基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Combining DEVS simulation and ontological modeling for hierarchical analysis of the SARS-CoV-2 replication
This article presents an hybrid and hierarchical model in which two modeling and simulation approaches, discrete event system specification simulation (DEVS) and semantic technologies, were used together in order to help in the analysis of a major healthcare problem, the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). Indeed, the complexity of the SARS-CoV-2 replication process, and the range of hierarchical scales over which it interacts with cellular components (extending from genomic and transcriptomic to proteomic and metabolomic scales), and the intricate way in which they are interwoven, make its understanding very challenging. It is therefore crucial to model the different scales of the replication process, by taking into account all interactions with the infected cell. By combining the advantages of both DEVS simulation and ontological modeling, we propose a hierarchical ontology-based DEVS simulation model of the SARS-CoV-2 viral replication at both the micro-molecular (proteomic and metabolomic) and macro-molecular (genomic and transcriptomic) scales. First, we demonstrate the usefulness of combining DEVS simulation and semantic technologies in a common modeling framework to face the complexity of the SARS-CoV-2 viral replication at different scales. Second, the modeling and simulation of the SARS-CoV-2 replication process on different levels provide valuable information on the different stages of the virus’s life cycle and lays the foundation for a system to anticipate future mutations selected by the virus.
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来源期刊
CiteScore
3.50
自引率
31.20%
发文量
60
审稿时长
3 months
期刊介绍: SIMULATION is a peer-reviewed journal, which covers subjects including the modelling and simulation of: computer networking and communications, high performance computers, real-time systems, mobile and intelligent agents, simulation software, and language design, system engineering and design, aerospace, traffic systems, microelectronics, robotics, mechatronics, and air traffic and chemistry, physics, biology, medicine, biomedicine, sociology, and cognition.
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