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>
>Colleagues, I'm looking for a program to conduct a triads analysis.  Any
>recommendations?
>Thanks
>Wayne Baker

There is the "motif finder" program that Milo et al. used in their 
two provocative papers in Science.  The motif finder will do triadic 
census, as well as look for all four-node formations.  It is 
relatively straightforward to use.

The programs can be downloaded from:
  http://www.weizmann.ac.il/mcb/UriAlon/

The papers are:
1.	Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, 
Alon U. Network Motifs: Simple Building Blocks of Complex Networks. 
Science. 2002;298:824-827.
2.	Milo R, Itzkovitz S, Kashtan N, et al. Superfamilies of 
Evolved and Designed Networks. Science. 2004;303:1538-1542.

The cleverness of these papers comes from their use of simulated 
ensembles of networks of the same connectivity as the observed 
network.  But I haven't been able to convince myself as to what 
general classes of questions this ensemble approach provides the 
"right" null hypothesis, as opposed to simpler triadic census 
approaches.  I'd welcome advice.

best,
   Jack

-- 
-=-=-=-=-=-=-=-=-=-=-=-=-=-
Theodore J. Iwashyna, M.D., Ph.D.

Division of Pulmonary and Critical Care
Department of Medicine
Hospital of the University of Pennsylvania

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