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.

Schlagworte

flux balance analysis

network visualization

layout algorithm

graph layout

motion graph

DDC Class

570: Biowissenschaften, Biologie

Lizenz

https://creativecommons.org/licenses/by/2.0/

Name

1471-2105-14-322.pdf

Size

1.78 MB

Format

Adobe PDF

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