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]