Cytoscape: Software for Visualization and Analysis of Biological Networks
Cytoscape: Software for Visualization and Analysis of Biological Networks
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DOI：
10.1007/978-1-60761-987-1_18
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发表时间：
2011-01-01
期刊：
影响因子：
--
通讯作者：
Warscheid, Bettina
中科院分区：
文献类型：
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作者：
Kohl, Michael;Wiese, Sebastian;Warscheid, Bettina
在“ OMICS”研究（例如基因组学，转录组学，蛋白质组学和代谢组学）领域取得了重大进展，从而导致了大量的生物学数据。为了以易于解释的方式表示大型生物数据集，该信息经常被视为图形，即一组节点和边缘。节点是生物分子和边缘连接描述某种关系的节点的表示。显然，对基于计算机的可视化和生物学数据分析的基于计算机的援助的需求很高，生物学数据通常是异质性的，并从不同的源中检索。本章侧重于有助于对生物网络的视觉探索和分析的软件工具。讨论了此类计划的全球要求。使用广泛使用的Cytoscape工具来说明可视化软件的利用。注释部分提供了有关使用细胞尺度的其他信息。此外，要突出显示替代软件工具的特殊功能，以帮助研究人员为其特定要求选择足够的程序。
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.