NetworkAnalyzer: Computation and Visualization of Topological Parameters and Centrality Measures for Biological Networks

Yassen Assenov, Nadezhda Doncheva, Thomas Lengauer, and Mario Albrecht

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany

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


Cytoscape version: 2.6

Plugins to Load: NetworkAnalyzer (, IntActWSClient

GUI steps:

Describe each step (story), the GUI action to take, and probable remarks




Load Ataxins network

import network via IntActWSClient plugin: search for 'Lim'

Run NetworkAnalyzer

Plugins -> Network Analysis -> Analyze Network

Decide whether your network should be treated as directed or undirected

Explore network topology

click on the tabs to see the parameters and their distributions

Parameters are stored as node and edge attributes

change charts (scatter plot/histogram, axes, log scale, colors, zoom…) -> click 'chart settings', 'chart range'

fit function to chart -> click 'fit line' or 'fit power law'

export diagrams as graphics -> click 'export chart'

export data for spread sheets -> click 'export data'

Visualize topological parameters

click 'visualize computed parameters' -> map degree to node size, map clustering coefficient to node color, map edge betweenness to edge color/size

Save network statistics

click 'save statistics'

network parameters can be re-imported at any time -> network analysis has to be done only once

Network modifications

Plugins -> Network Modifications -> Remove Duplicated Edges

Plugins -> Network Modifications -> Remove Self-Loops

Extract connected components of network

Plugins -> Network Modifications -> Connected Components. Select a connected component of interest to be displayed as separate network.

Data / Session Files: ataxins_network.sif, ataxins.netstats, NetworkAnalyzer_Session.cys

Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

NetworkAnalyzerRecipe (last edited 2009-02-12 01:03:50 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux