生物代謝網(wǎng)絡(luò)的混合Petri網(wǎng)建模與分析
發(fā)布時(shí)間：2018-07-21 21:31
【摘要】：生物代謝一直是生命科學(xué)研究的基礎(chǔ)領(lǐng)域之一,對生物代謝網(wǎng)絡(luò)中眾多反應(yīng)的途徑、作用、原理等進(jìn)行透徹研究,對生物學(xué)、醫(yī)學(xué)甚至是制藥學(xué)等等各種領(lǐng)域都有著重要的意義。生物代謝過程微觀、復(fù)雜,如果能夠直觀地表現(xiàn)出來,將為代謝網(wǎng)絡(luò)的研究提供極大便利。如何直觀、準(zhǔn)確的建立生物代謝網(wǎng)絡(luò)的模型一直是一個(gè)難點(diǎn)與研究焦點(diǎn)。傳統(tǒng)的生物建模方法存在適用范圍窄、無法對代謝網(wǎng)絡(luò)更為微小的反應(yīng)過程建模、局限于僅有單個(gè)反應(yīng)方程或者能夠線性相加的數(shù)個(gè)方程的建模、與代謝網(wǎng)絡(luò)結(jié)構(gòu)契合度低等缺陷�；趯@些缺陷的改進(jìn),以及對生物代謝網(wǎng)絡(luò)建模分析的特殊需求,本文進(jìn)行了生物代謝網(wǎng)絡(luò)的混合Petri網(wǎng)建模研究,具體研究工作有以下幾點(diǎn):(1)對Petri網(wǎng)在建模領(lǐng)域的理論發(fā)展歷程進(jìn)行了總結(jié),并對國內(nèi)外使用Petri網(wǎng)理論對生化領(lǐng)域進(jìn)行建模分析的研究現(xiàn)狀做了歸納,概述了研究生化網(wǎng)絡(luò)、代謝網(wǎng)絡(luò)的眾多理論、思路、方法以及對Petri網(wǎng)理論的優(yōu)化擴(kuò)展。(2)使用混合Petri網(wǎng)進(jìn)行建模分析。提出了一個(gè)生物代謝網(wǎng)絡(luò)HPN建模的詳細(xì)建模步驟,使用該建模步驟,能夠?qū)崿F(xiàn)在缺乏生物代謝相關(guān)理論知識、生化試驗(yàn)環(huán)境與條件的情況下進(jìn)行生化建模。并以三羧酸循環(huán)為實(shí)例,依照提出的建模步驟建立了混合Petri網(wǎng)系統(tǒng)模型,使用建模軟件SNOOPY2.0對建立的模型進(jìn)行仿真模擬與分析。證實(shí)了該理論的正確性與可行性。(3)在三羧酸循環(huán)混合Petri網(wǎng)的基礎(chǔ)上,本文對已建立的HPN模型做了進(jìn)一步擴(kuò)展,獲取了一種適用于生物代謝網(wǎng)絡(luò)建模的混合函數(shù)Petri網(wǎng)模型,并據(jù)此建立了三羧酸循環(huán)的HFPN模型。接著提出一個(gè)生物代謝網(wǎng)絡(luò)反應(yīng)過程的狀態(tài)標(biāo)識輸出算法,實(shí)現(xiàn)了對反應(yīng)過程的監(jiān)控及數(shù)據(jù)獲取,最后在三羧酸循環(huán)模型中以一簡例證明了該算法的可行性。
[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.
【學(xué)位授予單位】：天津科技大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2016
【分類號】：Q591;TP301.1
本文編號：2136919
[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.
【學(xué)位授予單位】：天津科技大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2016
【分類號】：Q591;TP301.1
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