Cytoscape

Cytoscape Project Web Site

This is an ISB goose, simple in design, intended for displaying and exploring networks.

Some features of Cytoscape:

1. Nodes and edges may have any kind, and any number, of data attributes attached.
2. These data attributes are used to control the visual attributes -- so that, for instance, a gene with high expression ratio and low pvalue may appear dark red and proportionately large.
3. Edge confidence scores and node association types (i.e., protein-DNA, protein-protein) are often used to display different widths, styles, and colors of edges. Networks and name lists are most commonly broadcast to and from Cytoscape from other geese in a gaggle.

File format

Cytoscape uses SIF or GML files. A SIF file can be as simple as three tab delimited columns as shown here:

VNG6476G    pdass   VNG0016H
VNG6476G    pdass   VNG0017H
VNG6476G    pdass   VNG0019H
...

The first and third columns become nodes in the network, while the second column describes a connection or interaction between two nodes. See the Cytoscape website for more details.

Note

We plan to adopt Cytoscape 2.5 in the Gaggle as soon as the CyGoose plugin is updated to use the current Gaggle API; we are using Cytoscape 1.1 in the meantime.