BioFNet: biological functional network database for analysis and synthesis of biological systems
BioFNet: biological functional network database for analysis and synthesis of biological systems
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DOI：
10.1093/bib/bbt048
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发表时间：
2014-09-01
影响因子：
9.5
通讯作者：
Takata, Takenori
中科院分区：
文献类型：
--
作者：
Kurata, Hiroyuki;Maeda, Kazuhiro;Takata, Takenori
在合成生物学和系统生物学中，自下而上的方法可以用来构建复杂的、模块化的、层次化的生物网络结构。要分析或设计这样的网络，关键是要了解网络结构和功能之间的关系，即生物部分或生物分子组装成构件或功能网络的机制。功能网络被定义为执行特定功能的生物分子的子网络。了解构建功能网络的机制将有助于开发一种分析大规模网络结构的方法，并设计出执行目标功能的健壮生物电路。我们提出了一个生物功能网络数据库，称为BioFNet，它可以在分子相互作用的水平上覆盖整个细胞。BioFNet在实现功能网络数学模型的仿真程序、可视化仿真结果等方面具有优势。它为生化网络的合理设计和理解功能网络如何组装以创建复杂的高级功能提供了可靠的基础，这将揭示分子结构背后的设计原则。
In synthetic biology and systems biology, a bottom-up approach can be used to construct a complex, modular, hierarchical structure of biological networks. To analyze or design such networks, it is critical to understand the relationship between network structure and function, the mechanism through which biological parts or biomolecules are assembled into building blocks or functional networks. A functional network is defined as a subnetwork of biomolecules that performs a particular function. Understanding the mechanism of building functional networks would help develop a methodology for analyzing the structure of large-scale networks and design a robust biological circuit to perform a target function. We propose a biological functional network database, named BioFNet, which can cover the whole cell at the level of molecular interactions. The BioFNet takes an advantage in implementing the simulation program for the mathematical models of the functional networks, visualizing the simulated results. It presents a sound basis for rational design of biochemical networks and for understanding how functional networks are assembled to create complex high-level functions, which would reveal design principles underlying molecular architectures.