---------- Forwarded message ---------- Date: Mon, 5 Nov 2001 09:28:05 +0000 (GMT) From: Ewan Birney <birney@ebi.ac.uk> To: Elia Stupka <elia@fugu-sg.org> Cc: Bioperl <bioperl-l@bioperl.org> Subject: Re: [Bioperl-l] Genquire 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 > > Elia > > -- > ****************************** > * http://www.ebi.ac.uk/~elia * > * tel: +65 874 1467 * > * mobile: +65 90307613 * > * fax: +65 777 0402 * > ****************************** > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-l > ----------------------------------------------------------------- Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420 <birney@ebi.ac.uk>. ----------------------------------------------------------------- _______________________________________________ Bioperl-l mailing list Bioperl-l@bioperl.org http://bioperl.org/mailman/listinfo/bioperl-l