Table 1

Compare ProteoLens against Cytoscape, VisANT and BiologicalNetworks.

ProteoLens

Cytoscape

VisANT

BiologicalNetworks

Graph manipulation

yFiles

yFiles and GINY

In house

Cytoscape

Laying out Network Algorithm

force-directed, Radial Layout hierarchical, circular, orthogonal

More than 13 kinds of layout styles.

force-directed

grid, circular, force-directed

Drawing appearance

node shape/colour/border/label, edge colour/style/direction/label

node shape/colour/border/label, edge colour/style/direction/label

node shape/colour/size

node shape/colour/border/label, edge colour/style/direction/label

Filters

select nodes/links according to properties or using SQL statement for table attributes selecting directly

select nodes/links according to properties (SQL-like)

Several 'select' filters available

select nodes/links according to properties (SQL-like)

Expand/Collapse nodes

expand node neighbours

Plug-in

expand node neighbours

Database Incline

Common Relational database

Plug-in

Predictome

PathSys

System Requirements

Java stand-alone

Java applet or stand-alone

Java applet

JSP (Java Server Pages)

Save

GML,XML session

GML,SIF

network with layout

save all work as projects

Imports

Text, GML, XML, Oracle or PostgreSQL

text, GML, expression matrix, OBO

PSI-MI, BioPAX, KGML, network relations (text)

microarray data (Stanford,Affymetrix,TIGR,GenePix), SBML, SIF, PSI-MI, BioPAX

Exports

JPEG,BMP, GML network relations, Node lists, selections node lists (text)

graphical file, SVG, GML, network relations (text)

PSI-MI, BioPAX, SVG, JPEG, network relations (text)

GIF, JPEG, SWF, PDF, PNG, PostScript, RAW, SVG, BMP

Comments & other features

Embedding the SQL query make its software more flexible to suit powerful bioinformatics experts usage

The importance of Cytoscape is its solid support for plug-in, growing number of which is available.

Statistics ability for topological characteristic analysis and integrating several biological database

Integrated visualization and analysis of expression data.

*A summary of attributes of Cytoscape, VisANT and BiologicalNetworks as presented in detail by Matthew Suderman et al in review. [26]

Huan et al. BMC Bioinformatics 2008 9(Suppl 9):S5   doi:10.1186/1471-2105-9-S9-S5