Table 1.

Comparison of VisANT against Cytoscpe and Osprey

	VisANT	Cytoscape	Osprey
Graph Manipulation	Developed in house	Based on yWorks package	Developed in house
Data Generalization*	Node can either be Protein/Gene, chemical compound, KEGG pathway	Protein/Gene/Compound	Protein/Gene
Input	• Up-to-date Predictome database, both experimental/computation data • On-line network file saved per user • Tab-delimited user data through copy/paste	• Local file with its own format for both network and expression data.	• Up-to-date Grid database with experimental data only • local file with its own format
Output	• On line saving of work space per user • Export as tab-delimited file • Jpg image	• Local file • Image printing	• Local file • Image printing • Vector graph
Search	• On-line searching using either name, GI number, ORF ID, KEGG pathway ID etc.	• Search node name on the graph	• Search node name on the graph
Network Operation	• Various layouts • Network motif detection including feed-forward, feedback, shortest path, auto-regulation etc.	• Various layouts	• Various layouts
Filtering	• Filtering the data with the different methods • Compare different data sets • Select nodes with certain range of connections	• Flexible filters with different attributes of node and edge	• Filtering the data with the different methods/resources • Compare different data sets
Multi-species	• Support 66 species • Enable orthology searching against Human genome	N/A	Support 4 species
Integration	• KEGG database • Genbank database • SGD database	• Go database	• Go database
Run Mode	• On-line java applet	• Stand-alone application	• On-line java applet • Stand-alone application
Java version	1.1 above	1.4 above	1.4 above
License	Open source	Open source	Commercial, free to academy

*All three programs can display any string as a node. The components listed in this row are those that have biological annotations