From: VisANT: an online visualization and analysis tool for biological interaction data
 | 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 |