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Table 1 Comparison of VisANT against Cytoscpe and Osprey

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