生物代谢网络的混合Petri网建模与分析

发布时间：2018-07-21 21:31

【摘要】：生物代谢一直是生命科学研究的基础领域之一,对生物代谢网络中众多反应的途径、作用、原理等进行透彻研究,对生物学、医学甚至是制药学等等各种领域都有着重要的意义。生物代谢过程微观、复杂,如果能够直观地表现出来,将为代谢网络的研究提供极大便利。如何直观、准确的建立生物代谢网络的模型一直是一个难点与研究焦点。传统的生物建模方法存在适用范围窄、无法对代谢网络更为微小的反应过程建模、局限于仅有单个反应方程或者能够线性相加的数个方程的建模、与代谢网络结构契合度低等缺陷。基于对这些缺陷的改进,以及对生物代谢网络建模分析的特殊需求,本文进行了生物代谢网络的混合Petri网建模研究,具体研究工作有以下几点:(1)对Petri网在建模领域的理论发展历程进行了总结,并对国内外使用Petri网理论对生化领域进行建模分析的研究现状做了归纳,概述了研究生化网络、代谢网络的众多理论、思路、方法以及对Petri网理论的优化扩展。(2)使用混合Petri网进行建模分析。提出了一个生物代谢网络HPN建模的详细建模步骤,使用该建模步骤,能够实现在缺乏生物代谢相关理论知识、生化试验环境与条件的情况下进行生化建模。并以三羧酸循环为实例,依照提出的建模步骤建立了混合Petri网系统模型,使用建模软件SNOOPY2.0对建立的模型进行仿真模拟与分析。证实了该理论的正确性与可行性。(3)在三羧酸循环混合Petri网的基础上,本文对已建立的HPN模型做了进一步扩展,获取了一种适用于生物代谢网络建模的混合函数Petri网模型,并据此建立了三羧酸循环的HFPN模型。接着提出一个生物代谢网络反应过程的状态标识输出算法,实现了对反应过程的监控及数据获取,最后在三羧酸循环模型中以一简例证明了该算法的可行性。
[Abstract]:Biological metabolism has always been one of the basic fields of life science research. We have thoroughly studied the pathways, functions and principles of many reactions in biological metabolic networks, and made a thorough study of biology, Medicine and even pharmaceutical science and other fields are of great significance. The microcosmic and complex biological metabolic process, if demonstrated intuitively, will greatly facilitate the study of metabolic networks. How to establish the model of biological metabolic network intuitively and accurately is always a difficulty and research focus. The traditional biological modeling method has a narrow range of application, which can not model the smaller reaction process of the metabolic network, and is limited to the modeling of only a single reaction equation or several equations that can be added linearly. Defects such as low compatibility with metabolic network structure. Based on the improvement of these defects and the special requirements of modeling and analysis of biological metabolic network, the hybrid Petri net modeling of biological metabolism network is studied in this paper. The specific research works are as follows: (1) the development of Petri net theory in the field of modeling is summarized, and the present situation of modeling and analysis of biochemical field using Petri net theory at home and abroad is summarized, and the postgraduate network is summarized. There are many theories, ideas, methods and optimization extensions of metabolic networks. (2) using hybrid Petri nets to model and analyze. In this paper, a detailed modeling procedure for HPN modeling of biological metabolism network is proposed. Using this modeling step, biochemical modeling can be realized without the relevant theoretical knowledge of biological metabolism and the environment and conditions of biochemistry test. Taking the tricarboxylic acid cycle as an example, a hybrid Petri net system model is established according to the proposed modeling steps. The modeling software SNOOPY2.0 is used to simulate and analyze the established model. The correctness and feasibility of the theory are verified. (3) based on the tricarboxylic acid cycle hybrid Petri net, the HPN model has been further extended, and a hybrid function Petri net model suitable for the modeling of biological metabolism network has been obtained. The HFPN model of tricarboxylic acid cycle was established. Then a state label output algorithm for the reaction process of biological metabolism network is proposed to monitor the reaction process and obtain data. Finally, the feasibility of the algorithm is proved by a simple example in the tricarboxylic acid cycle model.
【学位授予单位】：天津科技大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：Q591;TP301.1

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