[Biojava-l] SequenceDBInstallation

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Tue, 04 Jul 2000 20:27:45 +0100

Thomas Down wrote:

> I'm also starting to wonder if it might not be time to look

> into the Java Naming and Directories Interface (JNDI) which
> is included in JDK1.3, and available as an optional package for
> earlier Javas.  The big API for this has always scared me a little
> bit, but I've been and had another look today, and perhaps it's
> not as bad as it first looks, at least for simple applications.
> In the medium term, I'd be happy to look into writing a biological
> JNDI service provider, maybe as an optional add-on on top of the
> BioJava core.
> Any other views on this?


For what it's worth (which you might think isn't that much given that you're
the one volunteering to do the coding!)...

o Definitely JNDI is the way to go here - you're right, it's not as bad as
you first thought!

o I'm not so sure you need to write your own JNDI service provder.  In fact,
it would be cool if biojava wasn't tied to underlying service providers
(different people will have different requirements in this regard). That is,
JNDI is an interface - so you should be able to transparently swap out
underling service implementations, as long as you don't want to do anything
too funky.   As a start (and may be as an end), an LDAP service provider
might let you do a lot of what you want (it seems what you're suggesting is
essentially read-orientated, and LDAP is pretty good at that).

o Finally, if it was me, in thinking about how to store information in any
service provider, I would consider the fact that I might want non-Java
people to be able to access the information in it.  In other words,
serialized Java objects perhaps might not be the best way to go in terms of
persisting objects, say. Just thought I'd mention, 'cos I know you're fond
of Java Serialization ;-)

OK, that's the end of my two cents on this topic...

Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK