Cytoscape WikiIt would be really useful for to Cytoscape output the properties of any given network - for example:
- mean shortest path
- degree distribution
- average number of interaction partners
- top 10 interacting proteins
- clustering coefficient
- topological coefficient
- etc...
(From Guy Warner via bug tracker - Nov.4.2005)
MarcioSilva on 2005-11-08: One can look at [http://jung.sourceforge.net/ JUNG] code. It can do lots of network analysis and its licence is [http://www.opensource.org/licenses/bsd-license.php BSD], what means Cytoscape developers can borrow some code from there (if the credit is given). I think if it was [http://www.opensource.org/licenses/gpl-license.php GPL] it wouldn't be possible because Cytoscape licence is [http://www.opensource.org/licenses/lgpl-license.php LGPL] and work based on GPL should be GPL. This is not a problem with [http://www.opensource.org/licenses/bsd-license.php BSD] licenced software (but I may be wrong as I am not an expert in licences 
).
From [http://jung.sourceforge.net/ JUNG] website:
The current distribution of JUNG includes implementations of a number of algorithms from graph theory, data mining, and social network analysis, such as routines for clustering, decomposition, optimization, random graph generation, statistical analysis, and calculation of network distances, flows, and importance measures (centrality, PageRank, HITS, etc.).