Guide to viewing the network files in Cytoscape

The network and complex graphics are generated with the Cytoscape program. This page will guide you through the installation and setup of Cytoscape to view the networks and complexes as shown in the article. This guide applies to Cytoscape version 2.3.

If you do not have cytoscape installed go to www.cytoscape.org and download and install the appropriate version for your platform. Follow the installation instructions on the Cytoscape site.

The *.sif files contain the network files, but additional information is found in the *.noa and *.eda files. To generate the same visual schemes for network layout, node colour, node shape and line width, the "lage_karlberg_et_al.props" file is needed. Download the network files you need, or preferably: all of them in a .zip format into a new directory (right-click the link and choose "save as...ok").

Start Cytoscape

Import the network/complex:

Choose "File → import → network" and choose the *.sif file you downloaded

Import node attributes:

Choose "File → import → node attributes" and choose the *.noa files you downloaded or Press the "Import attributes from file" button on the "Node Attribute Browser" on "CytoPanel 2"

Import edge attributes:

Choose "File → import → edge attributes" and choose the *.eda files you downloaded or Press the "Import attributes from file" button on the "Edge Attribute Browser" on "CytoPanel 2" To view the loaded attributes in "CytoPanel 2" press the green arrow in either "Node Attribute Browser" or "Edge Attribute Browser".

Load the visual styles used in the article figures:

Choose "File → import → Vizmap property file" and select the lage_karlberg_et_al.props file downloaded. Once loaded, select the "lage_karlberg_et_al" visual style from the "Change the current visual style" box.