++ Cytoscape Portal

Cytoscape software can make network graphs.

Here's a paper describing how to analyze some data with Cytoscape
-Topological analysis and interactive visualization of biological networks and protein structures
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-11-13\Topological analysis and interactive visualization of biological networks and protein structures.pdf"

-neat looking paper: Analysis and Visualization of Biological Networks with Cytoscape


Cytoscape looks like a good tool for making protein network graphs.
-Sheri used this in her sperm proteome research with the ClueGO plugin (the ClueGO plugin handles the gene ontology annotations)


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see also
-[Network portal 11-11-13]