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3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape

Qi Wang14, Biao Tang2, Lifu Song3, Biao Ren14, Qun Liang4, Feng Xie1, Ying Zhuo1, Xueting Liu1* and Lixin Zhang1*

Author Affiliations

1 Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China

2 State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200433, People’s Republic of China

3 Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany

4 University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China

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BMC Bioinformatics 2013, 14:322  doi:10.1186/1471-2105-14-322

Published: 14 November 2013



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.


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.


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.