[Bioperl-l] protein networks

Allen Day allenday at ucla.edu
Fri Feb 6 11:44:20 EST 2004


To my knowledge, nothing exists in bioperl.  If you were to implement
something, http://psidev.sf.net would be a good place to start.  The
Proteomics Standards Initiative, of which DIP is a part, is working to
develop standard formats for proteomics data.


On Fri, 6 Feb 2004, Richard Adams wrote:

> Hi,
> I was wondering if anyone has written or is writing any modules to deal 
> with protein interaction networks?
> E.g., to read in from a DIP flatfile or XML, or other such interaction 
> information source
> and to have methods such as
> get_number_of_interactors()
> get_interactor_ids()
> clustering_coefficient()
> path_length(from, to)
> degree()
> mean_path_length().
> etc.
> Richard

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