Bioperl: RE: On Commercial OODBs for XML

[Otillar, Robert {~Palo Alto}]

	Thanks for a highly informative letter; I appreciate your sharing
your experience.
	I have been told a few things about ObjectStore & would appreciate
your comments:

*	The WinNT version is a easily usable & trustable product? The WinNT
version of Object Store on SGI is 'one revision behind and requires a fair
bit of sysadmin knowledge to tune the SGI, but that the NT version is much
easier to support & use.
*	Major vendors are using ObjectStore; is it as easy & reliable as
they claim? NetGenics uses ObjectStore with the C++ engine, coupled with a
Java API. This configuration is robust (?), perhaps due to Java's built-in
memory-handling rather than C++'s user-controlled memory handling. The
NetGenics software team seems quite knowlegable and, in a demo, their
product looked well designed and stable.
*	How does ObjectStore's reliabliity & usability compare to the
alternatives? ObjectStore looks much easier to administrate than
Objectivity, given the GUI admin tools on their web-site. I believe I've
heard that ObjectStore is easy to administrate on NT, but can't recall a
concrete reference guaranteeing this is true.
*	Any experience with Objectivity, Poet, or other systems?


*	Do you have reccommendations on other systems: reliable, easily
learned and administrated, reasonably fast persistent object storage & query
tool (for use with BioPerl)? 
*				se Oracle8's object-relational interface and
design 2000 tools. (FYI Oracle 8 on linux is now free to developers <
http://technet.oracle.com/ >).


Thanks,
	Bobby O

> -----Original Message-----
> From:	Lincoln Stein [SMTP:lstein@cshl.org]
> Sent:	Thursday, January 14, 1999 6:44 AM
> To:	Otillar, Robert {~Palo Alto}
> Cc:	David J. States; 'vsns-bcd-perl@lists.uni-bielefeld.de'
> Subject:	On Commercial OODBs for XML RE: Bioperl: XML/BioPerl
> 
> 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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