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Table 1 Compare ProteoLens against Cytoscape, VisANT and BiologicalNetworks.

From: ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining

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