University of Padova, Padova.
IEEE/ACM Trans Comput Biol Bioinform. 2012;9(2):592-600. doi: 10.1109/TCBB.2011.116. Epub 2011 Aug 18.
Studying biological networks at topological level is a major issue in computational biology studies and simulation is often used in this context, either to assess reverse engineering algorithms or to investigate how topological properties depend on network parameters. In both contexts, it is desirable for a topology simulator to reproduce the current knowledge on biological networks, to be able to generate a number of networks with the same properties and to be flexible with respect to the possibility to mimic networks of different organisms. We propose a biological network topology simulator, SimBioNeT, in which module structures of different type and size are replicated at different level of network organization and interconnected, so to obtain the desired degree distribution, e.g., scale free, and a clustering coefficient constant with the number of nodes in the network, a typical characteristic of biological networks. Empirical assessment of the ability of the simulator to reproduce characteristic properties of biological network and comparison with E. coli and S. cerevisiae transcriptional networks demonstrates the effectiveness of our proposal.
研究拓扑层面的生物网络是计算生物学研究中的一个主要问题，在这种情况下，通常会进行模拟，要么是为了评估反向工程算法，要么是为了研究拓扑性质如何依赖于网络参数。在这两种情况下，拓扑模拟器都希望能够再现生物网络的现有知识，能够生成具有相同属性的许多网络，并能够灵活地模拟不同生物体的网络。我们提出了一种生物网络拓扑模拟器 SimBioNeT，其中不同类型和大小的模块结构在不同的网络组织层次上进行复制和相互连接，从而获得所需的度分布，例如，无标度的，以及与网络中节点数成正比的聚类系数，这是生物网络的典型特征。对模拟器再现生物网络特征性质的能力的实证评估，并与大肠杆菌和酿酒酵母转录网络进行比较，证明了我们建议的有效性。
