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Table 1 A comparison between available 3D network visualization tools

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

Program name File format Operating system Programming language Source code availability Time course data support Layout algorithm Performance*
Arena3D [7] Arena3D Platform-Independent Java yes yes Layered 2,000 nodes, 10,000 edges
BioLayout SIF, XML, TXT, GraphML, Matrix, Expression Platform-Independent Java yes yes Fruchterman-Rheingold 500 nodes, 2,500 edges
Express 3D [5]
FORG3D [8] FORG3D Windows, Linux and Mac OS X C++ yes no Force-directed 4,000 nodes, 40,000 edges
Vaa3D [4] TIFF, SWC, CSV Windows, Linux and Mac OS X C++ yes yes Location based 2,500 textured nodes and edges
Wilmascope 3D [6] Wilmascope, GML Platform-Independent Java yes yes Force-directed, etc. 2,000 nodes, 5,000 edges
3DScapeCS any format supported by Cytoscape Platform-Independent Java yes yes Multilevel Force-directed 10,000 nodes, 250,000 edges
  1. *Approximate network size measured with minimum frames per second (fps) which enables smooth manipulations (drag, rotate, etc.) on an eight core Intel Xeon 2.13 GHz workstation with an on-board Matrox G200 graphics card.