[Bioperl-l] Workbench3 internals
Mon, 12 Feb 2001 14:13:55 -0600 (CST)
I am thinking about what I'd like for the next version of Workbench, and
one of the things is a better object/database relationship. It's not bad
now, just repetitive, and not as easily extensible as I'd like.
So, if I'm going to abstract the database interface layer, I am thinking
of integrating it with bioperl. Bioperl is very flat-file heavy, but in
this era, with mysql free and open, it makes sense to have easy save
capabilities to a mysql database. I think we can do it.
So, is it a good idea? Am I re-inventing the wheel? And finally, how
much needs to be stored in the database? Do I need to come up with a
blast report schema, for example? That might be nice, but it might be
very bloated. Schema for hsp's, complicated transcript objects, etc...
I know ensembl has gone down this road, but they haven't played for
generality. I would like this to be a painless addition to bioperl, given
a mysql installation.
Comments? Feedback? Death threats?
Plant Biotechnology Institute
National Research Council of Canada