[Biopython-dev] interaction networks in biopython

[Ed Schofield]

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