[Bioperl-l] [RFC] Interolog::Walk

Giuseppe Gallone G.Gallone at sms.ed.ac.uk
Thu Aug 19 08:42:28 EDT 2010


Dear Siddhartha,

glad to hear this might be helpful. As for the bioperl-network package 
you mention, thank for you for mentioning that. I gave a quick look to 
its documentation and looks like a much deeper and more complex effort 
than what I have in my package. I've actually been using a lot the 
package Graph on which it seems to be based and found it very helpful.

I'm not sure if the network routines in my module overlap with it 
though: all I do in my package is parse the dataset, filtering out only 
what requested to build a cytoscape SIF file and optionally some 
cytoscape NOA attribute files, as requested by the cytoscape 
specification in

http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats

instead it looks like  bioperl-network actually builds some kind of 
internal representation of the network for further manipulation in Perl, 
if I understand it correctly?

Kind regards
Giuseppe

On 19/08/10 01:28, Siddhartha Basu wrote:

> Sounds interesting. I am currently playing around with a perl based webapp for displaying interactome
> using cytoscapeweb. Depending how your design pans out,  would be happy to
> use your module as a backend analysis layer. And on a related note,  you
> might want to have a look at bioperl-network and if there is any overlap
> might be worth contributing.
>
> -siddhartha
>


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