[Bioperl-l] contributing? sure!

Fernan Aguero fernan@inti.gov.ar
Tue, 11 Jul 2000 16:11:56 -0300

I have some newbie questions about the following:

>bioperl-db is an effort to provide sequence database access and support
>for updateable sequences (and the annotations) outside of the core bioperl
>read-only seq db support.
>Currently this is being implemented using the Ensembl db structure (with
>some additional tables) on a mysql db server.  The ultimate goal for
>ensembl-lite (in my mind at least) is a reasonable framework for
>small/midsized laboratories to store their genomic data and access to the
>analysis pipelines (a lite-r version than the standard ensembl pipeline). 
>When the DAS standard is completed we would also like to make an
>ensembl-lite a DAS server.
>AceDB support as well would be nice to allow users to access data in the
>ensembl-lite system transparently if it is in the mysql db, and acedb
>file/server, or a remote web db (GenBank, others ... ).  Other ideas or
>additions will be welcome.
>I am in the mid stages of the updatableseqdb implementation, and still
>designing the rest of the structures.  Suggestions, volunteers, support is
>welcome of course.

We are currently trying to implement some automated framework to do 
analysis on sequences. Our approach uses PostgreSQL and some Perl 
scripts to get sequence data in the database, do the analysis on them 
and store results again in the DB.
i) is this what ensembl does?
ii) what is the developing status of bioperl-db?
iii) any reasons to choose MySQL instead of PostgreSQL? I know that 
the first is faster than the latter...any other?
We have settled ourselves with PostgreSQL due to its ability to do 
subqueries. Although we don't have any subqueries now that we need to 
do, we thought that this capability could be useful. Any comments on 

And a proposal:
My experience with Perl is limited, although i can usually get away 
with what i want to do. If this description fits a volunteer, we can 
start talking about what I can do for bioperl-db. Or maybe i can help 
with some other task...


Lic. Fernan Aguero                                        Tel: 
(54-11) 4752-0021
Instituto de Investigaciones Biotecnologicas              Fax: 
(54-11) 4752-9639
Universidad Nacional de General San Martin