[BioSQL-l] Re: [Volunteer] I would like to get involved...

[Hilmar Lapp]

Jim,

I'm the lead developer on biosql. I'm cc'ing the biosql list just in 
case someone has a better suggestion right away.

How do Chris' comments sound to you? There is no BioSQL for Oracle 
How-To yet, just a rough installation and instantiation guide that I 
hacked together a while ago. We've just had a post where somebody would 
have greatly benefitted from a more extensive documentation of the 
Oracle version.

Although MySQL is probably the main platform most biosql-users will 
use, I know that a fair number of people also run it on Postgres. The 
shop I'm with is an Oracle shop, so that is the platform I myself 
mostly work with. If you check out the repository and look into the 
stuff under sql/biosql-ora, you'll find some things that are probably 
9i specific, but you may be able to cut those things out to get it 
instantiated under 8i. We could then document what needs to be changed 
for 8i.

As for perl, I'm also the lead developer on bioperl-db, which is the 
perl language binding for biosql. It establishes persistence for 
bioperl objects to/from a biosql schema. It's an OR mapper essentially, 
and so it's no surprise that it's become a fairly complex piece of 
code. There is a fair number of things to be done for bioperl-db, 
ranging from documentation to actual code. Just let me know what you 
want to get yourself into.

	-hilmar

On Monday, July 28, 2003, at 05:27  PM, Chris Dagdigian wrote:

>
> James,
>
> There is an offshoot project of bioperl called 'biosql' which is part 
> of another project we are calling 'OBDA' (open bio database access).
>
> A big part of biosql/OBDA is providing schema, docs, scripts, tools 
> and documentation to people who want to store sequence info in 
> relational databases. We generally target mySQL but I know that others 
> are working on maintaining Oracle compatability as well.
>
> Would you be interesting in something like that? Hilmar and Jason 
> would know better than I if someone has already written the "BioSQL 
> for Oracle" Howto document.  If this does not exist than we need one > :)
>
> We also are in dire need for help keeping content up to date on the 
> biosql/obda websites.
>
> Any of this sound interesting? Would you be willing to contribute to 
> biosql/obda as a Oracle guru? The first steps would be helping with 
> documentation and general "Howto" for Oracle but future steps could 
> involve coding oracle-specific scripts/utilities etc.
>
> Regards,
> Chris
> open-bio.org
>
>
> Jim Barnett wrote:
>
>> Hello,
>> I am very fluent with PERL, and ORACLE and I'm hoping I can get 
>> involved.  I
>> would be willing to do code testing, or code writing.  If given a 
>> task to
>> carry out I have the time to do it, using PERL, regular expressions, 
>> sql,
>> oracle or whatever...  I have an Oracle 8 server setup and can use 
>> that for
>> any testing, and I've been using activestate perl, and microsoft iis 
>> as a
>> webserver.  I'm also fluent in UNIX/LINUX and could adjust to that
>> environment quickly --  So please let me know how I can get 
>> involved...
>> Thanks, James Barnett
>> jbarnett at frictionless.com
>> barnettjames at comcast.net
>> _______________________________________________
>> Volunteer mailing list
>> Volunteer at open-bio.org
>> http://open-bio.org/mailman/listinfo/volunteer
>
>
> -- 
> Chris Dagdigian, <dag at sonsorol.org>
> BioTeam Inc. - Independent Bio-IT & Informatics consulting
> Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
> PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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