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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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