On Commercial OODBs for XML RE: Bioperl: XML/BioPerl

[Lincoln Stein]

Otillar, Robert {~Palo Alto} writes:
 > 
 > 
 > > Is anyone aware of plans on the part of the database organizations to
 > > serve 
 > > XML?
 > > 
 > 		I've been giving thought to XML as representation standard
 > to couple with a persistent storage database for genomic data. I thought you
 > might be interested in a little of what I've found out about the commercial
 > OODB products.
 > 
 > 		Object Designs, Inc., (www.odi.com) is in late beta-testing
 > of their Excelon XML database/server, part of the ObjectStore line of
 > products. Of interest:
 > 		ObjectStore has PERL drivers on CPAN. (The supported
 > bindings are in C++ and Java).

I had five years of experience writing biological databases with
ObjectStore using the C++ binding, and can state unequivocally that
I'd never do it again.  When a C++ object is persistent, all dangling
references, memory leaks, twice-deallocated pointers, and incompletely
constructed objects are persistent too.  This gives any application
programmer the ability to corrupt the database.  I haven't tried the
Java or Perl drivers; perhaps they're better.

ObjectStore is also a real administrative hassle to set up and
maintain.  Getting the system up and running means mastering a slew of
obscure environment variables and strangely-named configuration files.
Unfortunately the voluminous manuals are poorly written and badly
organized.  On the bright side, ObjectStore's help desk is excellent,
and their technical support outstanding.

ObjectStore's competitors are right when they warn about scaleability.
ObjectStore is designed around clever uses of the Unix mmap() system
call.  Unfortunately different systems have arbitrary limits on the
amount of disk space that can be mapped in this way.  On SunOS the
limit is hit at about 1 gigabyte (don't know about Solaris).  On IRIX
systems this was 2 gig.  This really hurts.  The limit is extremely
high on 64-bit architectures like Digital Unix/Alpha, but when we
tried to run the appropriate version on alphas, it was too buggy to
use.

Lincoln

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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