[Biopython-dev] interaction networks in biopython

Yair Benita yair.benita at gmail.com
Tue May 15 19:25:27 UTC 2007

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 GRAPHVIZ. If
anyone wants to suggest anything else, please do.


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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