Su Gang, Morris John H, Demchak Barry, Bader Gary D
Molecular Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan.
Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-24. doi: 10.1002/0471250953.bi0813s47.
Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users.
Cytoscape是用于可视化探索由蛋白质、基因和其他类型相互作用组成的生物医学网络的最流行的开源软件工具之一。它为研究人员提供了一个多功能且交互式的可视化界面，用于探索由各种注释和实验数据支持的复杂生物互连，从而促进诸如预测基因功能和构建通路等研究任务。Cytoscape提供加载、可视化、搜索、过滤和保存网络的核心功能，并且数百个应用程序扩展了此功能以满足特定的研究需求。相对于以前的版本，最新一代的Cytoscape（3.0及更高版本）在功能、用户界面和性能方面有了实质性的改进。本协议旨在通过针对Cytoscape基本功能的特定协议，帮助新用户快速上手，例如安装Cytoscape和Cytoscape应用程序、加载数据、可视化和浏览网络、可视化网络相关数据（属性）以及识别聚类。它还突出了对有经验的用户有益的新功能。
