The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies. This visualization method allows for easy comparison of different experiments in the context of the network or pathway. Supplementary data are available at Bioinformatics online. RESULTS:We developed a 3D Cytoscape Client/Server (3DScapeCS) plugin, which adopted Cytoscape in interpreting different types of data, and UbiGraph for three-dimensional visualization. CyLineUp is a Cytoscape 3 app for the projection of high-throughput measurement data from multiple experiments/samples on a network or pathway map using small multiples. DyNetViewer is freely available with tutorials at the Cytoscape (3.4+) App Store (). AbstractSummary: CytoCom is an interactive plugin for Cytoscape that can be used to search, explore, analyse and visualize human disease comorbidity network. Moreover, visualization of different topological variation of nodes and clusters over time enables users to quickly identify the most variations across many network states. The current version of DyNetViewer consists of four different dynamic network construction methods, twelve topological variation analysis methods and four clustering algorithms. Here, we develop DyNetViewer, a Cytoscape application that provides a range of functionalities for the construction, analysis and visualization of dynamic protein–protein interaction networks. The construction and analysis of dynamic molecular networks can elucidate dynamic cellular mechanisms of different biological functions and provide a chance to understand complex diseases at the systems level. 1597-1599 ISSN: 1460-2059 Subject: algorithms, bioinformatics, protein-protein interactions, topology Abstract: The molecular interactions in a cell are varying with time and surrounded environmental cues. DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization Author: Min Li, Jie Yang, Fang-Xiang Wu, Yi Pan, Jianxin Wang, Jonathan Wren Source: Bioinformatics 2018 v.34 no.9 pp.

Dynamic network csv cytoscape