[Bioperl-l] Genquire

[Ewan Birney]

On Mon, 5 Nov 2001, Elia Stupka wrote:

> Great stuff! I've been thinking of using the GUI with bioperl-db for a
> long time, never got around it. We will be installing it very soon over
> here and evaluating it. Just wandering, is the db very different from
> bioperl-db? I feel we should think about converging the two or if Genquire
> is clearly better, chuck some of it away,etc. In short, we should make
> sure users that come fresh to the bio group are pointed to only one place
> for handling sequences with a database, let's think about it, what are
> your views?

When I first looked at GenQuire I felt it could not support "interface
level" database transfer/access - and, in addition, it bound the database
to the object at a very tight granularity (each edit on the object
triggers an update/insert into the database).


Bioperl-db was written with a more "ensembl like" in-memory business
object which collaborates with a database adaptor, and the database
adaptor can ->store() any Bio::SeqI compliant object. I didn't see that
sort of functionality in GenQuire when I looked.


I was also a little worried about the "chat" table in GenQuire, which
seemed a little out-of-scope!


Mark and Dave may well have moved it on from there and provided a better
all-over database. Elia - I'd trust your call on what the best way forward
was: either

   (a) maintain bioperl-db and genquire separately for separate tasks (no
shame in this). Off hand I'd guess

       bioperl-db = relational database equivalent of storing flat file
EMBL/GenBank, but with much better querying, response time and data
managements

       genquire = relational database for annotation/curation of DNA
sequence

       (ensembl = relation database for automatic annotation and large
scale pipelining)


  (b) Refactor one into the other: probably the only sensible thing is to
move bioperl-db into GenQuire and Dave and Mark have too much
code/investment into GenQuire to unpick and put on to a different backend.




Just because they all use SQL backends doesn't mean they all do the same
thing of course...



ewan





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