Biological networks are important tools for understanding the complexity and functionality of biological systems, and their dynamic analysis can reveal the dynamic behavior of biological processes. However, the high complexity and diversity of biological networks pose urgent challenges for research, requiring the development and application of advanced computational methods. This study reviews the different types of biological networks and their functional roles in biology, and explores in detail network dynamics calculation methods including graph theory, agent-based modeling, differential equations, etc. In addition, we also focus on dynamic modeling of gene regulatory networks, protein-protein interaction networks, and metabolic networks, analyzing the applications and limitations of these methods in practical biological systems. In order to provide a comprehensive reference for researchers in the field of biological network dynamics.
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Li et al. (2024) studied this question.