[BioPython] Biopython hackathon

[Chris Fields]

On Mar 14, 2007, at 6:43 PM, Ann Loraine wrote:

> ...
> (2) Another request is for a Python interface to the Bio::Db::SQL
> database schema described in:
>
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
> cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12368253.
>
> The part that seems particularly valuable would be code that to
> construct the location-based queries.

Did you mean Bio::DB::GFF?  AFAIK Lincoln is moving stuff over to a  
newer system that better facilitates GFF3, namely  
Bio::DB::SeqFeature.  I'm not sure how well Bio::DB::GFF is supported  
currently.

> My apologies if this already exists -- if yes, please let me know
> where I can find it!!

You can find out about the current state of GBrowse affairs by  
emailing the GBrowse mail list.  Here's the sourceforge link:

http://sourceforge.net/mailarchive/forum.php?forum_id=31947

Scott and Lincoln can indicate where their current focus is re: GFF3  
and sequence feature database development.

chris

> All the best,
>
> Ann Loraine


Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign