[Biopython-dev] interaction networks in biopython

Steve Lianoglou lists.steve at arachnedesign.net
Tue May 15 19:56:46 UTC 2007


On May 15, 2007, at 3:25 PM, Yair Benita wrote:

> I would be happy to contribute to this too.
> Currently I have a python script that uses HPRD to generate protein  
> protein
> interaction maps. I have deferent filtering methods to display only  
> classes
> of proteins or only links to a specific kegg pathway. It will need  
> a bit of
> work before I can submit this to CVS. As for drawing the map, I am  
> currently
> generating a dot file that can be converted to an image using  
> anyone wants to suggest anything else, please do.

I've been using NetworkX[1] to play w/ networks/graphs interactively.  
You can display them if you have matplotlib installed, and can save  
the graphs to dot format as well.


[1] NetworkX: https://networkx.lanl.gov/wiki

> Yair
> on 5/15/07 2:37 PM, Ed Schofield at edschofield at gmail.com wrote:
>> On 5/15/07, Jake Feala <jfeala at gmail.com> wrote:
>>> Hello Biopython people -
>>> With all the new research in genome-wide cellular interaction
>>> networks I was a little surprised not to see much support for these
>>> type of data in Biopython.  I know that Bioperl has a networks  
>>> package
>>> that looks like the kind of thing that I would love to also see in
>>> Python for all the obvious reasons.
>>> First - has this already been done and I missed it?  All I could  
>>> find
>>> were a few scattered and application-specific scripts across the  
>>> web,
>>> plus the Pathway package in BioPython.
>>> If not, then would there be any interest in development along these
>>> lines?  A while back I wrote a few scripts that parse interaction
>>> datasets, stick them into a MySQL database, and retrieve the
>>> interactions into a Network object that can be used to analyze the
>>> graph of nodes and links.  I would be glad to update these to fit  
>>> into
>>> the biopython framework, as it would be useful to my own research.
>>> One caveat is that I am an engineering PhD student and my  
>>> programming
>>> skills are mostly self-taught beyond two Java courses, so I might  
>>> need
>>> a little guidance in testing and preparing the code for  
>>> distribution.
>>> I have only ever written code for my own personal research but I  
>>> think
>>> my style is decent and I would love to get better.
>>> Any opinion or advice?
>> This would interest me too; I'd be glad to have such functionality in
>> BioPython. I can offer you some guidance on Python, packaging and
>> testing, and (if you need it) use of external array packages.
>> -- Ed
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