3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape.
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.
Qi
Q
Wang
Biao
B
Tang
Lifu
L
Song
Biao
B
Ren
Qun
Q
Liang
Feng
F
Xie
Ying
Y
Zhuo
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. liuxueting_cn@hotmail.com.
Xueting
X
Liu
Lixin
L
Zhang
D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D016208:Databases, Factual; D021621:Imaging, Three-Dimensional; D013058:Mass Spectrometry; D008954:Models, Biological; D025941:Protein Interaction Mapping; D012984:Software; D014584:User-Computer Interface