[Bioperl-l] Contributing to biomoose

Chris Fields cjfields at illinois.edu
Tue Jul 21 18:00:09 UTC 2009

On Jul 20, 2009, at 11:03 PM, Robert Buels wrote:

> Siddhartha Basu wrote:
>> Of course it there is a core biomoose distribution,  then that  
>> namespace
>> makes a lot of sense for non-core modules. The philosophy also goes
>> nicely with the organization of current MooseX modules. And if  
>> something
>> in Bio::MooseX(really futuristic) becomes heavily important it can be
>> integrated into the core Bio::Moose namespace. The same thing is also
>> happening with MooseX::Attribute module.
> Bio::Moose isn't a good namespace for the long term.  For  
> experimenting around with Moosey implementation techniques it's  
> fine, but before you guys go putting TOO much code into it, consider  
> what its future is going to be.  Moose is an implementation  
> technology, and modules should be named for what they do, not how  
> they're implemented.

True, but in the short term this will have to do, primarily to stay  
out of the way of similarly names BioPerl namespace (for the time  
being it enables us to run a few initial benchmarks comparing  
implementations between the two).  Not too many other namespaces like  
Bio that work.

If we want something shorter we could move it to something else once  
we have a decent enough name.  Maybe Alces (genus name for Moose)?   
Seems kinda lame...

> We already know Moose is far superior for organizing and expressing  
> designs, so what I would be shooting for here would be some deep,  
> focused implementations of certain aspects.  It's starting to sound  
> like it's getting a little bigger than just playing around.
> Rob

Not really.  We have to test out a few initial implementations in  
order to see how they compare to the BioPerl versions (memory- and  
speed-wise).  PrimarySeq is essentially done except for small things,  
so I may start working on some prim. benchmarks.


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