Kohl Michael, Wiese Sebastian, Warscheid Bettina
Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
Methods Mol Biol. 2011;696:291-303. doi: 10.1007/978-1-60761-987-1_18.
Substantial progress has been made in the field of "omics" research (e.g., Genomics, Transcriptomics, Proteomics, and Metabolomics), leading to a vast amount of biological data. In order to represent large biological data sets in an easily interpretable manner, this information is frequently visualized as graphs, i.e., a set of nodes and edges. Nodes are representations of biological molecules and edges connect the nodes depicting some kind of relationship. Obviously, there is a high demand for computer-based assistance for both visualization and analysis of biological data, which are often heterogeneous and retrieved from different sources. This chapter focuses on software tools that assist in visual exploration and analysis of biological networks. Global requirements for such programs are discussed. Utilization of visualization software is exemplified using the widely used Cytoscape tool. Additional information about the use of Cytoscape is provided in the Notes section. Furthermore, special features of alternative software tools are highlighted in order to assist researchers in the choice of an adequate program for their specific requirements.
“组学”研究领域（如基因组学、转录组学、蛋白质组学和代谢组学）已取得重大进展，产生了大量生物学数据。为了以易于解释的方式呈现大型生物学数据集，这些信息常被可视化为图形，即一组节点和边。节点代表生物分子，边连接节点以描绘某种关系。显然，对于生物数据的可视化和分析，对基于计算机的辅助有很高需求，这些数据通常是异构的且来自不同来源。本章重点介绍有助于生物网络可视化探索和分析的软件工具。讨论了此类程序的总体要求。使用广泛使用的Cytoscape工具举例说明了可视化软件的使用。注释部分提供了有关Cytoscape使用的更多信息。此外，还强调了替代软件工具的特殊功能，以帮助研究人员根据其特定需求选择合适的程序。
