[Bioperl-l] Bio::Moose is now....

Chris Fields cjfields at illinois.edu
Fri Jul 31 22:22:17 EDT 2009

I think, before any CPAN release, I want to nip the monolith in the  
bud.  Just have Meta/Root and simple interfaces (roles) describing  
classes in Biome, actual implementations or other additions going into  
BiomeX::*.  The current Biome::Location/Annotation/etc would  
eventually be moved into their own BiomeX repos.  Bundle with  
Task::Biome (maybe add some automated bundling options).  Sound  

I'll try to get a ROADMAP up next week.


On Jul 31, 2009, at 9:53 AM, Robert Buels wrote:

> I think this sounds great.  GREAT news about the Biome::PrimarySeq  
> performance.
> Rob
> Chris Fields wrote:
>> Biome!  This makes the most sense to me; as Mark points out the  
>> name works as an appropriate acronym (BioPerl with Metaclass  
>> Extensions), as well as a biome being (per wikipedia):
>> "a climatically and geographically defined areas of ecologically  
>> similar climatic conditions such as communities of plants, animals,  
>> and soil organisms ... often referred to as ecosystems".
>> Seems a fitting name for a open-source project.  I'll be moving the  
>> namespace over to Biome over the next couple of days on github.   
>> Now I owe Mark some beer...
>> Now, for extensions, should I assume this will eventually be  
>> BioPerl2 (and thus use BioX::*)?  Or stick with BiomeX::*?
>> chris
>> PS: Just a quick benchmark for the current Bio::Moose::PrimarySeq  
>> implementation (we don't have SeqIO working as of yet, so the  
>> benchmark script does the heavy lifting):
>> http://gist.github.com/158317
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> -- 
> 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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