Validation and Analysis of Metabolic Pathways Using Petri Nets
Validation and Analysis of Metabolic Pathways Using Petri Nets
复制标题
使用 Petri 网验证和分析代谢途径
DOI：
10.1007/978-981-16-1740-9_30
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
G. Singh
中科院分区：
文献类型：
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作者：
Sakshi Gupta;Sunita Kumawat;G. Singh
Petri网已被广泛用于建模和分析各种具有并发性、并行性和冲突性的专家系统。由于代谢网络的复杂性和密集性，需要对这些系统进行建模以了解其拓扑结构。Petri网是一种广泛使用的数学工具，用于建模和研究代谢途径。在这里，我们已经解释了如何利用PN的分析技术来模拟，验证和研究代谢途径的行为。我们认为，生物合成的聚羟基脂肪酸酯（PHAs）的存在下的克雷布斯循环为例来解释的验证和分析过程中使用Petri网。PHA是由细菌在营养缺乏的条件下合成的，并作为能量储存材料储存。当葡萄糖是PHA生物合成的主要碳源时，克雷布斯循环是竞争途径。所获得的结果提供了一个有效的数学模型，以确认一些已知的属性，他们的代谢途径，也提供了一些结果，该系统将如何在克雷布斯循环的存在下表现。该模型可用于进一步的研究，以获得新的见解，在这一途径沿着与其他竞争途径。如果这种Petri网方法与一些实验方法相结合，对代谢途径的分析可能会更有用。
Petri nets (PNs) have been widely utilized for modelling and analysing different expert systems which are characterized by concurrency, parallelism and conflicts. Due to the complex and dense nature of metabolic networks, modelling of these systems is needed to understand their topology. Petri net is one of the extensively used mathematical tools for modelling and studying metabolic pathways. Here, we have explained how analysis techniques of PNs can be exploited to simulate, validate and study the behaviour of metabolic pathways. We considered the biosynthesis of polyhydroxyalkanoates (PHAs) in the presence of krebs cycle for illustration to explain the validation and analysis process using Petri net. PHAs are synthesized by bacteria during nutrient lack conditions and are stored as energy storage materials. Krebs cycle is the competing pathway when glucose is the main source of carbon in PHA biosynthesis. The obtained results provide a valid mathematical model for confirming some of the known properties about their metabolic pathway and also provide some results on how the system will behave in the presence of krebs cycle. The model can be used in further studies to get new insights in this pathway along with other competing pathways. Analysis of the metabolic pathways can be more useful if this Petri net approach is related with some experimental approach.