[Open-bio-l] Re: [Bioperl-l] -db and -gui?

[Thomas Down]

On Sun, Apr 21, 2002 at 10:39:17AM -0400, Jason Stajich wrote:
> 
> I would really like to push for all toolkits supporting the biosql schema
> before BOSC in August so that we can move the OBDA work along - is that a
> reasonable request for everyone?  Perhaps if the devs are having trouble
> finding time to work on things they could report where they are and
> what needs to get done so other potential volunteers can know where they
> can help?  Not sure who the biopython rep is - but I assume Thomas was
> still biojava-biosql pointman and Chris M was the bioperl-biosql lead.
> Can you guys chime in on where things are and where they need to go for a
> stable or alpha release?

Hi...

The Java implementation seems to be working out okay.  It's using
the Cape Town schema version, and has been tested by various
people, including a lot of the people at the BioJava bootcamp
last month.  There's a baseline version in the BioJava 1.21
release, although there have been a few improvements/optimizations
since then.

Here's a vague to-do list for it in case anyone's interested:

   - Replace stand-alone test scripts with JUnit (and a small
     config file to specify database details).

   - Implement a paging system for more efficient handling of huge
     feature tables (I've got a plan for this, but not fully
     implemented yet).

   - Expose references in the database using the OpenBQS object
     model.

   - Ports to other databases (Oracle, anyone?)

Hope this gives you a better idea of where we are in BioJava-land,

    Thomas.