3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape
© Wang et al.; licensee BioMed Central Ltd. 2013
Received: 30 August 2013
Accepted: 11 November 2013
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.
A comparison between available 3D network visualization tools
Source code availability
Time course data support
2,000 nodes, 10,000 edges
SIF, XML, TXT, GraphML, Matrix, Expression
500 nodes, 2,500 edges
Express 3D 
Windows, Linux and Mac OS X
4,000 nodes, 40,000 edges
TIFF, SWC, CSV
Windows, Linux and Mac OS X
2,500 textured nodes and edges
Wilmascope 3D 
2,000 nodes, 5,000 edges
any format supported by Cytoscape
10,000 nodes, 250,000 edges
Visualization of three-dimensional networks
Additional file 4: The 3DscapeCS Movie - Basic Operation and Expression Data Visualization.(MP4 20 MB)
The layout algorithms are required to generate meaningful and aesthetic drawings of biological networks. The layout algorithm built in UbiGraph is force-directed based. It acts by balancing the repulsive force between nodes and attractive force from the edge. After several rounds of movement and annealing, it generates aesthetically pleasing graph layouts with all edges of nearly equal length. The force-directed layout algorithm implemented in Cytoscape has a complexity of O(N3) and low-quality local drawing , it is only suitable for networks containing up to several hundred nodes. Other global force-directed algorithms such as Fruchterman-Reingold  experience the same bottleneck. Therefore local force-directed algorithms such as Fast Multipole Multilevel Method (FM3)  and Multilevel layout algorithm  have been developed. Hereby we adopted the multilevel layout algorithm in UbiGraph for larger networks. In this approach, the network is partitioned into sub-networks. Only forces within the scope of sub-networks are calculated, so that the final graph layout can be obtained in O(NlogN) runtime. Therefore it will greatly reduce the duration required to complete three-dimensional layout, which is significantly helpful in visualization of large-scale networks (Figure 1c).
Time-course data animation
3DScapeCS provides an approach for visualizing one network from multiple aspects by adopting parallel visualization. The Cytoscape network view can be simultaneously rendered in UbiGraph on multiple computer clients through network communication. Different clients can be set to visualize different aspects of the graph, either a reversal of perspective, or another time-point from a time-course animation. Unlike CytoscapeRPC , which use XML-RPC to modify networks in Cytoscape from clients, UbiGraph clients serve as XML-RPC servers in 3DScapeCS architecture. Therefore any changes made to the network view in Cytoscape, either change the size/colour of a node, or add/delete a node, can be reflected on all clients by synchronizing the network data between UbiGraph clients and Cytoscape.
Genome sequences scaffolding visualization
Dynamic visualization of metabolic flux data
Additional file 5: The 3DscapeCS Movie - Reaction Network Motion Visualization.(MP4 8 MB)
Additional file 6: The 3DscapeCS Movie - Substrate-product Network Motion Visualization.(MP4 8 MB)
Mass Spectrometry (MS) molecular network visualization
Additional file 7: The 3DscapeCS Movie - Motion Network Visualization of MS Experiments.(MP4 8 MB)
Detecting bubbles in De Bruijn graph
Three-dimensional visualization provides novel insights for Cytoscape. With time-course, colour, size, shape customization, 3DScapeCS can support up to seven dimensional data visualization, making it useful in presenting large-scale complex data. Although external renderers such as UbiGraph can add 3D functionalities to Cytoscape, the operations of network are limited in UbiGraph. For example, user can neither drag vertices or edges in the graph to set locations, nor set the parameters of the multilevel layout algorithm, which make it less effective in heterogeneous 3D data visualization. Therefore, in the future, a more powerful renderer featured with more layouts and subcellular localization networks, such as neuronal networks, should be implemented. Moreover, mobile devices such as iPad or Android Pad, which can be manipulated using fingers and gestures, are more suitable to manipulate 3D view. So it is also desirable to implement renderers on those platforms for wireless parallel visualization.
We have integrated UbiGraph and Cytoscape in 3DScapeCS. The 3D perspective not only guarantees user a greater experience in visualization, but also offers more insight into Cytoscape networks. Parallel motion graph is useful in visualizing data obtained with different conditions, as well as different aspects in a single experiment. Such functionalities give full play to their strength on a three-dimensional platform. Therefore 3DScapeCS has more advantages in large and/or complex network visualization as the study cases presented in previous paragraphs.
Availability and requirements
Project name: 3DScapeCS
Project home page: http://scape3d.sourceforge.net/
Operating system(s): Platform-independent.
Programming language: Java
Other requirements: Cytoscape v2.8, UbiGraph needs to be started as its renderer.
License: Lesser General Public License (LGPL).
Any restrictions to use by non-academics: None.
This work was supported in part by grants from the Ministry of Science and Technology of China (2013CB734004) and the National Natural Science Foundation of China (31100075, 81102362, 31170095, 31000004). LXZ is an Awardee for National Distinguished Young Scholar Program in China. We appreciate Dr. Pieter C. Dorrestein for providing Mass Spectrometry instruments in UCSD.
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