[Bioperl-l] Re: Contributing to biomoose

Siddhartha Basu sidd.basu at gmail.com
Tue Jul 21 01:56:55 UTC 2009

On Sun, 19 Jul 2009, Chris Fields wrote:

> I'm actually working on Bio::Moose::Annotation along with tests (I have 
> SimpleValue, Reference, Comment, Target, and DBLink working). I'll try 
> committing that tonight, but first I'll take a look at your code and try 
> to make sure ours merge properly. I don't see any conflicts thus far.
> A ROADMAP is a good idea; I'll definitely work towards that.  As for  
> specific modules, there are lots of places to start:
> Bio::Tree?
> Bio::Location?
> Bio::Align* and Bio::SimpleAlign (just the basic functionality)?
> SeqFeature?

Will start with Bio::Location then.

> The IO parsers should fall into place rather quickly once the basic  
> objects are in place, I wouldn't worry about them for the moment; we  
> need basic implementations and tests.  Bio::Annotation::Collection is  
> where I'm going next.
> Just make sure to 'use Bio::Moose' or 'use Bio::Moose::Role', and have  
> the namespace in Bio::Moose so it doesn't conflict with regular BioPerl, 
> e.g. 'Bio::Moose::Tree', roles maybe as 'Bio::Moose::Roles::Tree'.  We 
> will need to test these against their BioPerl counterparts sometime.

I will also try to put things in the wiki as i go along,  particularly
my understanding of the basic moose role/base classes that you have

> I'll also add an AUTHORS file, so add your name in when you can.
> chris
> PS: Based on our recent discussions on-list about breaking up BioPerl,  
> I'm wondering whether we'll need an eventual Bio::MooseX.  May be  
> something to think about.

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. 


> On Jul 19, 2009, at 9:23 PM, Siddhartha Basu wrote:
> > Hi chris,
> > I have forked your 'biomoose' git project and recently added bunch of
> > roles in my master in addition to the one (Annotation) you have  
> > already
> > merged. So far,  these were mostly interface centric module and were  
> > quite easy
> > to implement. Here is my github link ....
> > http://github.com/cybersiddhu/biomoose/tree/master
> >
> > Anyway,  i want to contribute with other module but wondering which  
> > other
> > modules would be a good target particularly leaving those out which
> > you/others are working or have plans to work on. Any
> > suggestions/ideas/roadmaps will be really helpful.
> >
> >
> > thanks,
> > -siddhartha
> >
> >
> >
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