BIOLOGICAL NETWORK EXPLORATION WITH CYTOSCAPE 3
By Gang Su, J. H. Morris, Barry Demchak, Gary D. Bader. Current Protocols in Bioinformatics, 2014
944 citations recorded by the source corpus.
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. Curr. Protoc. Bioinform. 47:8.13.1‐8.13.24. © 2014 by John Wiley & Sons, Inc.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/906947ee847fb92b45cf61876aff435d73a82489
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Citations in the corpus
- A new genome-mining tool redefines the lasso peptide biosynthetic landscape (2016, methodology): “Networks were visualized using the Organic layout within Cytoscape v. 3.2.0 52 and Adobe Illustrator (Supplementary Data Set 2).”
- NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (2019, methodology): “Firstly, Net-workAnalyst aims to provide a web-based tool for creating and visualizing biological networks to complement the widely used stand-alone tools such as Cytoscape (36).”