[Biopython-dev] interaction networks in biopython

Jake Feala jfeala at gmail.com
Tue May 15 16:42:30 UTC 2007

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?

-Jake Feala
Bioengineering Dept.
University of California, San Diego

More information about the Biopython-dev mailing list