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MarcioSilva on 2005-11-08: One can look at [http://jung.sourceforge.net/ JUNG] code. It can do lots of network analysis and their 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). From their 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.).'' |
It 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 their 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). From their 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.).