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 |