[Biojava-dev] BioJava code repository

[Andy Maule]

Thanks Richard,

That clears things up a bit. I'll look through the SVN repository, and see
what I can find.

Andy

-----Original Message-----
From: Richard Holland [mailto:richard.holland at ebi.ac.uk] 
Sent: 23 March 2006 14:33
To: Andy Maule
Cc: biojava-dev
Subject: Re: [Biojava-dev] BioJava code repository


The derkholm.net Subversion repository is the current version of
biojava-ensembl, which is a separate project from the main biojava found in
the open-bio.org CVS servers. Biojava-ensembl is maintained by Thomas Down
<td2 at sanger dot ac dot uk> and as far as I know is up-to-date to Ensembl
version 37.

To use the Subversion repository directly you just point the command- line
Subversion client at the same URL as the one you typed into your web
browser.

Dazzle was also written by Thomas Down but I'm not sure if he still
maintains it. Best to ask him directly.

cheers,
Richard

On Thu, 2006-03-23 at 12:50 +0000, Andy Maule wrote:
> Hi,
> 
> I'm looking for java applications that use Ensembl for a research 
> project. In particular I'm interested in seeing how applications have 
> been changed in response to changes in the schema of Ensembl. So I 
> need to look at the source code repositories, and I've been looking at 
> the biojava CVS.
> 
> For those who are interested the project involves predicting the 
> impact of database schema changes on applications. I'm going to use 
> the change history of the Ensembl schema to find an interesting schema 
> change(s) that will affect the application. I'm then going to run a 
> tool over the application to see if I can effectivley predict what 
> needs to be changed. I'm then going to compare the predicted changes 
> with the actual changes, to see if my analysis was correct. I'd be 
> more than happy to explain the project further if anyone would like to 
> know more.
> 
> As far as I can see Biojava is still using the schema for version 10 
> as shown in org.ensembl.db.sql.SQLDatabaseAdaptor10. This is only from 
> the CVS repository though.
> 
> Someone on the Ensembl mailing list pointed me to 
> http://www.derkholm.net/svn/repos and the dazzle project. Could anyone 
> fill me in on whether this repository is the latest version, and is 
> there someway I could access via subversion directly?
> 
> Also where can I now get information about Dazzle?
> 
> Thanks
> 
> Andy Maule
> 
> 
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-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------