Network Analyzer

Biological Use Case: Analyze a biological network and discover its topological properties.

Procedure

Note: The NetworkAnalyzer plugin now come pre-installed in Cytoscape versions 2.8 and above.

Go to File>Import>Network from web services and select IntAct Web Service Client under Data Source.
Search for Lim. When prompted with the results of the search, click Yes to create a network. Enter a name for the network.

Go to Plugins->Network Analysis->Analyze Network. Decide whether your network should be treated as directed or undirected. In the Lim example, treat the network as undirected.

Explore the network topology:
- Click on the tabs to see the parameters and their distributions. Parameters are stored as nodes and edge attributes.
- Change the charts (scatter plot/histogram, axes, log scale, colors, zoom...) by clicking chart settings, chart range.
- Fit the function to chart by clicking fit line or fit power law.
- Export the diagrams as graphics by clicking export chart.
- Export data for a spread sheet by clicking export data.
To visualize topological parameters, click Visualize Parameters. Select Degree for mapping node size, and ClusteringCoefficient for mapping node color.
Save network statistics by clicking save statistics. Network parameters can be re-imported at any time, and network analysis has to be done only once.
To make network modifications, click Plugins->Network Modifications->Remove Duplicated Edges or Plugins->Network Modifications->Remove Self-Loops.
To extract connected components of your network, click Plugins->Network Modifications->Connected Components. Select a connected component of interest to be displayed as a separate network.