[Bioperl-l] EST database w/postgresql

[Jason Stajich]

----- Original Message -----
From: "Ewan Birney" <birney@ebi.ac.uk>
To: "Charles Hauser" <chauser@acpub.duke.edu>; "Jason Stajich"
<jason@chg.mc.duke.edu>
Cc: <bioperl-l@bioperl.org>
Sent: Thursday, May 03, 2001 12:51 PM
Subject: Re: [Bioperl-l] EST database w/postgresql


> On Thu, 3 May 2001, Charles Hauser wrote:
>
> > Greetings,
> >
> > I am new to the list, and to perl so please excuse my shortcommings.
> > I need to set up a database (postgresql) to both manage and use for
> > web queries  EST data and associated blast results, tentative gene
> > and protein id's etc.  I was hoping some of you out there have done
> > just this and might offer up advice for table layout, pitfalls to
> > avoid etc. before I dive in.
>
>
> First off - do contact Jason Staijch, if you haven't already, as he is
> both at Duke and understands this area well and final is a cool guy...
>
Charles and I have talked - I wanted to point him towards bioperl for a
larger group of people with similar experiences.  I'm happy to sit down with
you once you've gleaned enough ideas or approaches from the list.

>
> Secondly - check out the bioperl-db cvs module from the anonymous cvs
> server (instructions at http://cvs.bioperl.org/). This will
>
>   (a) solve some of your problems
>
>   (b) give you an idea how to structure code/table bindings
>
>
> Thirdly - make sure you have really scoped the problem well with either
> yourself (if you are doing it for yourself) or your "customers" ie - teh
> people you are building it.
>
Can't overemphasize this!

>   - in this area I am a big proponent of Extreme Programming (XP) where
> you would offer to your customers a number of options taking roughly 2/3
> weeks to complete like:
>
http://www.extremeprogramming.org/

It has some minuses but has reasonable approaches.  Of course you're
probably sitting there going - I don't want to run a software shop I just
want to get this problem solved, but there are good techniques you can use
from XP to make life easier.

>    Parsing a BLAST result into a database and having a bare-bones web page
>   (notice - no intiation of the BLAST stuff remotely)
>
> Or
>
>    Uploading an EST via the web into the database
>
> Or
>
>    something else you can imagine taking 2/3 weeks (honest weeks, eg not
> ideal weeks when noone interrupts you and your network stays up 100% of
> the time)
>
>
> Let the customers choose which things to work on first -- it (a) keeps you
> focused on what they want (b) involves them in the decisions about what
> will work first and what second - they will get less pissed off that not
> everything works first time...
>
>
> Fourthly - decide if you want to implement "inside" bioperl-db or not -
> this depends mainly on your comfort level with bioperl, but I would be
> happy to see - for example - additional pieces of schema into bioperl-db
> to provide storage of BLAST results
>
>
>
> Finally - Do the first iteration - go back to customers and possibly this
> list - and stepwise build it up.
>
>
>
> I'm happy to help -as I am sure is Jason - on schema and code design for
> new bits of code either inside bioperl-db or completely outside.
>
Don't be afraid to invent your own solution but to use bioperl-db as a
backend for storing the sequence data.

>
>
> ewan
>
>
> >
> > Thanks,
> >
> > Charles
> > --
> > Dr.Charles Hauser
> > DCMB, LSRC Rm B328
> > Duke University
> > Durham NC 27708-1000
> > 919.613.8159 tel
> > chauser@duke.edu
> >
> > _______________________________________________
> > 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>.
> -----------------------------------------------------------------
>
>
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