[Bioperl-l] A new name for Bio::Moose?

Chris Mungall cjm at berkeleybop.org
Tue Jul 28 01:53:09 UTC 2009

On Jul 27, 2009, at 9:23 AM, Chris Fields wrote:

> Robert,
> Herein lies the namespace problem.  What namespace would we inhabit  
> with Bioperl 2?  Bio2::*?
> We can't place anything in Bio w/o running into potential problems  
> re: namespace collisions, both locally and on CPAN (yes, I do intend  
> on releasing to CPAN at some point).  Bio* primary maintainer is  
> BIOPERLML, so releasing a Bio::Annotation::Foo on CPAN would  
> potentially collide with any BioPerl Bio::Annotation::Foo as an  
> unauthorized release.  If all code is sequestered in  
> Bio::Moose::Annotation::Foo, we don't have a problem beyond it  
> requiring more typing, hence the request for a name change  
> (preferrably something short) ;>
> Anyway, for all intents and purposes, if everything works out it  
> will very likely become bioperl 2.0, and the old Bio::Moose (or  
> whatever) will be deprecated on CPAN in favor of this.  Until then,  
> it is simply a side project to explore the feasibility of moving to  
> a Moose-based framework.  We can then work on reimplementing the  
> various split-off Bio::* we have been discussing elsewhere.
> One main side benefit of doing this: it's incredibly freeing.  I'm  
> finding numerous places where we could optimize things in BioPerl,  
> even in the case should this not pan out.  For instance, memoize and  
> clone locations instead of creating everything de novo.  Annotations  
> and AnnotationCollections could be lightened considerably if the  
> proper framework were provided, something like Data::Stag or XPath.

As the author of Data::Stag and one-time proponent of less object-y  
more xml-y modeling I'd say instead go for something a bit more  
moosey. I have a feeling that it is possible to use the meta-level  
features of Moose to come up with a solution for annotations that  
would turn out to be (a) flexible, extensible and intuitive, with the  
right benefits from both strong and weak typing (b) mind-bogglingly  
complex. Not sure which. But if Bio::Moose is just for experimentation  
just now might be worth trying.

>  Also, I have found other instances that will be beneficial to a  
> perl6-based implementation (roles vs interfaces primarily).  I'll be  
> posting here and blogging about these along the way.
> chris
> On Jul 27, 2009, at 10:25 AM, Robert Buels wrote:
>> Bioperl 2.  If the Moose business doesn't work out, throw away the  
>> moose code and do something different.  But I think it would be  
>> good to christen it as the embryonic bioperl 2 to get some momentum  
>> around it.
>> Rob
>> Chris Fields wrote:
>>> All,
>>> Pushed by a recent suggestion by Robert, I am considering changing  
>>> the name of the Bio::Moose project to something simpler.  I would  
>>> like to steer away from naming this directly after the  
>>> implementation and have something simpler namespace-wise.
>>> I have thought of 'Alces' (the genus name for moose), which  
>>> indicates both the Bio aspect and the implementation in an more  
>>> indirect way (and is a bit shorter).  However, I would like to  
>>> solicit suggestions for alternatives.  The shorter the better, and  
>>> the 'winner' will receive a free beverage or so (on me) should we  
>>> meet!
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> -- 
>> Robert Buels
>> Bioinformatics Analyst, Sol Genomics Network
>> Boyce Thompson Institute for Plant Research
>> Tower Rd
>> Ithaca, NY  14853
>> Tel: 503-889-8539
>> rmb32 at cornell.edu
>> http://www.sgn.cornell.edu
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