[Bioperl-l] who, if anyone, "owns" Bio::

Rutger Vos rvosa at sfu.ca
Fri Jul 22 19:54:09 EDT 2005

Dear bioperlers,

for a while now, I've been working on a set of perl modules for 
phylogenetic analysis. Obviously, I would like other people to use these 
too (and perhaps contribute to development as well), and so I wish to 
upload them to the CPAN. The working title for the root name space has 
been "Phylo::" but I'd like to change this because - rightly - the perl 
community is hesitant towards a proliferation of top level name spaces. 
Also, I might wish to incorporate my work into the bioperl release (that 
is, if the core developers agree) because, well, fragmentation helps 
no-one. I am however on the fence on this second issue.

To help me understand these issues I direct the following questions to 
the folks in the know:

* is the Bio:: namespace reserved for BioPerl proper or can other people 
- if appropriate - use it as their top level name space, in the same way 
as, say, WWW:: or CGI::?

* Do modules that use the Bio:: namespace have to be part of the bioperl 
release? I for one think bioperl is wonderful, but it is mostly aimed at 
molecular biologists, and so a phylogeneticist or evolutionary biologist 
might not want to install the whole thing just to use peripheral 
functionality. After all, BioPerl is (with all due respect) starting to 
grow into a fairly monolithic install.

Basically, I'm curious whether it would be okay on your part if I 
submitted my work under the Bio:: namespace, but as separate installs, 
to the comprehensive perl archive network. Like I said, I am at this 
point not entirely of one mind w.r.t merging/contributing to bioperl 
proper - to be honest, I fear that might be a hairy proposition what 
with other modules possibly making assumptions about underlying data 
structures in the packages rather than following the advertised API and 
what not, but I'm certainly interested in discussing that also.

Looking forward to your replies!

Best wishes,


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

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