Table 1 Examples of network visualisation programs used in bioinformatics
Software | Description |
|---|---|
Pajek [37] | A visualisation and analysis application for large graphs, used primarily for social network analysis. |
GraphViz [38] | Implements a number of common graph layout algorithms. |
Otter [39] | A tool developed for visualisation of internet data. |
H3Viewer [40] | Provides layout and interactive navigation of graphs in three-dimensional hyperbolic space. |
Biolayout(Java) [41] | Higher-level biological networks (e.g. metabolic pathways and regulatory networks) may be visualised. Basic network statistics are reported. |
Osprey [42] | Builds data-rich graphical representations that are colour-coded for gene function and experimental interaction data. Web interfaces are used to retrieve up-to-date interaction data. |
Cytoscape [43] | Integrates PPI networks with microarray and other gene expression data. Allows analysis of such networks by filtering subsets of nodes or interactions. |
MAGE [44] | Used primarily in molecular modelling but has also been used to visualise networks. Produces three-dimensional images that can be zoomed and rotated in real time. |
VisANT [45] | Developed to provide interactive visual mining of biological interaction data sets. |
Java applet [46] | Displays protein interactions organised by network distance and biological function. |