Cytoscape Portal

2015-06-18

++ 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)

favorite layouts in Cytoscape: yfiles Organic layout, "Edge-weighted Spring Embedded layout", "Inverted self-organizing map layout", ""Edge-weighted force directed (Biolayout)""