千兆级的系统生物学:复杂、异质多细胞系统的大型多尺度模型

IF 3.4 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Arnau Montagud , Miguel Ponce-de-Leon , Alfonso Valencia
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引用次数: 18

摘要

通过解释和揭示疾病的机制,基于主体的建模在几个生物医学项目中证明了它的有用性。然而,在这些模型中处理的场景通常考虑少量细胞,缺乏细胞特异性特征和动态相互作用,并且具有简单的环境描述。需要能够对需要复杂设置的生物系统进行可扩展、真实尺寸模拟的工具,以使模拟更接近生物医学场景,从而能够捕获细胞间的异质性和系统范围内的新特性。为了提供千兆级(109个单元)的模拟,不同的工具已经实现了在高性能计算集群中运行的技术。我们在此回顾这些努力,并详细介绍了该领域需要关注的主要改进领域,以使模拟更接近于拥有数字双胞胎。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems

Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems

Agent-based modelling has proven its usefulness in several biomedical projects by explaining and uncovering mechanisms in diseases. Nevertheless, the scenarios addressed in these models usually consider a small number of cells, lack cell-specific characterisation and dynamic interactions and have a simplistic environment description. Tools that enable scalable, real-sized simulations of biological systems that require complex setups are needed to have simulations closer to biomedical scenarios that can capture cell-to-cell heterogeneity and system-wide emerging properties. To deliver simulations at the giga-scale (109 cells), different tools have implemented technologies to run in high-performance computing clusters. We hereby review these efforts and detail the main areas of improvement the field needs to focus on to have simulations that are a step closer to having digital twins.

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来源期刊
Current Opinion in Systems Biology
Current Opinion in Systems Biology Mathematics-Applied Mathematics
CiteScore
7.10
自引率
2.70%
发文量
20
期刊介绍: Current Opinion in Systems Biology is a new systematic review journal that aims to provide specialists with a unique and educational platform to keep up-to-date with the expanding volume of information published in the field of Systems Biology. It publishes polished, concise and timely systematic reviews and opinion articles. In addition to describing recent trends, the authors are encouraged to give their subjective opinion on the topics discussed. As this is such a broad discipline, we have determined themed sections each of which is reviewed once a year. The following areas will be covered by Current Opinion in Systems Biology: -Genomics and Epigenomics -Gene Regulation -Metabolic Networks -Cancer and Systemic Diseases -Mathematical Modelling -Big Data Acquisition and Analysis -Systems Pharmacology and Physiology -Synthetic Biology -Stem Cells, Development, and Differentiation -Systems Biology of Mold Organisms -Systems Immunology and Host-Pathogen Interaction -Systems Ecology and Evolution
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