= 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.

'''__Recipe__'''

''__Cytoscape version__'': 2.6

''__Plugins to Load__'': NetworkAnalyzer (http://med.bioinf.mpi-inf.mpg.de/netanalyzer/), IntActWSClient

''__GUI steps__'':

Describe each step (story), the GUI action to take, and probable remarks
|| ''Story'' || ''Action'' || ''Remarks'' ||
||Load Ataxins network ||import network via IntActWSClient plugin: search for 'Lim' || ||
||<style="vertical-align: top;">Run NetworkAnalyzer ||<style="vertical-align: top;">Plugins -> Network Analysis -> Analyze Network ||<style="vertical-align: top;">Decide whether your network should be treated as directed or undirected ||
||<style="vertical-align: top;">Explore network topology ||<style="vertical-align: top;">click on the tabs to see the parameters and their distributions ||<style="vertical-align: top;">Parameters are stored as node and edge attributes ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;">change charts (scatter plot/histogram, axes, log scale, colors, zoom…) -> click 'chart settings', 'chart range' ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;">fit function to chart -> click 'fit line' or 'fit power law' ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;">export diagrams as graphics -> click 'export chart' ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;">export data for spread sheets -> click 'export data' ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Visualize topological parameters ||<style="vertical-align: top;">click 'visualize computed parameters' -> map degree to node size, map clustering coefficient to node color, map edge betweenness to edge color/size ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Save network statistics ||<style="vertical-align: top;">click 'save statistics' ||<style="vertical-align: top;">network parameters can be re-imported at any time -> network analysis has to be done only once ||
||<style="vertical-align: top;">Network modifications ||<style="vertical-align: top;">Plugins -> Network Modifications -> Remove Duplicated Edges ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;">Plugins -> Network Modifications -> Remove Self-Loops ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Extract connected components of network ||<style="vertical-align: top;">Plugins -> Network Modifications -> Connected Components. Select a connected component of interest to be displayed as separate network. ||<style="vertical-align: top;"> ||


'''__Data / Session Files__''': [[attachment:ataxins_network.sif]], [[attachment:ataxins.netstats]], [[attachment:NetworkAnalyzer_Session.cys]]

'''__Presentation__''': Attach your presentation

'''__Webstart__''': Attach a webstart

'''__Video__''': Attach a video link