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

Hu et al. BMC Bioinformatics 2004 5:17   doi:10.1186/1471-2105-5-17