[Bioperl-l] Contributing to biomoose

Chris Fields cjfields at illinois.edu
Mon Jul 20 04:22:41 UTC 2009

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::Align* and Bio::SimpleAlign (just the basic functionality)?

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'll also add an AUTHORS file, so add your name in when you can.


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.

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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