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  • Title: 3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape.
    Author: Wang Q, Tang B, Song L, Ren B, Liang Q, Xie F, Zhuo Y, Liu X, Zhang L.
    Journal: BMC Bioinformatics; 2013 Nov 14; 14():322. PubMed ID: 24225050.
    Abstract:
    BACKGROUND: The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-dimensional visualization tools. 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. The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies. CONCLUSIONS: Evaluation on several experimental data using 3DScapeCS and its special features, including multilevel graph layout, time-course data animation, and parallel visualization has proven its usefulness in visualizing complex data and help to make insightful conclusions.
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