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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.