Hybrid Petri net representation of gene regulatory network.
Hybrid Petri net representation of gene regulatory network.
复制标题
基因调控网络的混合 Petri 网表示。
DOI：
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发表时间：
1999
影响因子：
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通讯作者：
S. Miyano
中科院分区：
文献类型：
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作者：
H. Matsuno;Atsushi Doi;Masao Nagasaki;S. Miyano
因此，提供一种既能实现生物学家直观性又能保持计算能力通用性的基因调控网络表示方法具有重要意义。在本文中，我们提出了一种方法，利用混合Petri网（HPN）表示基因调控网络。HPN是Petri网的一种扩展，在计算机科学和工程领域中，Petri网已被用来表示包括随机系统在内的多种系统。由于HPN具有连续和离散元件，因此它可以轻松处理生物因素，如蛋白质和mRNA浓度。我们证明，通过使用HPN，有可能以自然的方式将生物事实翻译成HPN。还应该强调的是，我们采用分层方法构建λ噬菌体的遗传开关机制，该机制是通过使用HPNs实现的。HPN的这种层次化方法使得基于生物学事实的基因调控网络中的组件的排列变得更容易，并为我们提供了对网络的前瞻性看法。我们还显示了一些计算结果的λ噬菌体机制，模拟和观察通过实施HPN在目前可用的工具的蛋白质动力学。
It is important to provide a representation method of gene regulatory networks which realizes the intuitions of biologists while keeping the universality in its computational ability. In this paper, we propose a method to exploit hybrid Petri net (HPN) for representing gene regulatory networks. The HPN is an extension of Petri nets which have been used to represent many kinds of systems including stochastic ones in the field of computer sciences and engineerings. Since the HPN has continuous and discrete elements, it can easily handle biological factors such as protein and mRNA concentrations. We demonstrate that, by using HPNs, it is possible to translate biological facts into HPNs in a natural manner. It should be also emphasized that a hierarchical approach is taken for our construction of the genetic switch mechanism of lambda phage which is realized by using HPNs. This hierarchical approach with HPNs makes easier the arrangement of the components in the gene regulatory network based on the biological facts and provides us a prospective view of the network. We also show some computational results of the protein dynamics of the lambda phage mechanism that is simulated and observed by implementing the HPN on a currently available tool.