[Bioperl-l] BioCorba and phylogenetic trees

Jason Stajich jason.stajich at duke.edu
Wed Oct 12 14:11:14 EDT 2005

On Oct 3, 2005, at 10:40 AM, Rutger Vos wrote:

> Dear all,
> I am curious about the following:
> * what's the status of BioCorba, and how does it relate to BioPerl
It was a good idea but CORBA + WAN just doesn't work.  And really  
nobody really ended up ever having a real use case where they wanted  
to have BioJava server but wanted to run Bioperl on it or vice versa  
(or s/Perl/Python/ in there).  There are client/server libraries for  
wrapping and accessing objects in the three languages, but that  
development stopped years ago and the APIs of the projects have  
continued to evolve so I don't know if the libraries are compatible  
any more.

> * have bioperl-corba-clients and/or bioperl-corba-servers  
> succesfully been deployed on Win32? Using CORBA::ORBit?
Yes i believe so, but don't quote me on that, it was years ago when  
we actually went for full testing client/server stuff.  CORBA::ORBit  
on linux of course worked fine.

> * are there IDLs for tree objects/data structures in BioCorba?
When we started there were no tree objects in BioPerl, I don't know  
if the OMG project ended up with that or not.  I have stepped away  
from all of this two or three years ago so I don't really know what  
has been going on.

I think a lot of people would argue for SOAP over CORBA -- this  
certainly seems to be the trend in what is going on.  But I really  
don't do distributed/web services so am not the right person to comment.

> Some background: I'm "the perl guy" in this project: http:// 
> www.phylo.org
> We are looking to integrate phylogenetics software using corba.  
> It'd be good if we were compatible with BioPerl, hence the questions.
> Cheers,
> Rutger
> -- 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> Rutger Vos, PhD. candidate
> Department of Biological Sciences
> Simon Fraser University
> 8888 University Drive
> Burnaby, BC, V5A1S6
> Phone: 604-291-5625 Fax: 604-291-3496
> Personal site: http://www.sfu.ca/~rvosa
> FAB* lab: http://www.sfu.ca/~fabstar
> Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++
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Jason Stajich
Duke University

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