[Bioperl-l] Interest in Bio::Community modules

Florent Angly florent.angly at gmail.com
Sun Nov 27 23:35:31 EST 2011

Hi all,

I have been thinking about starting a set of Perl modules that would 
useful for (microbial) ecologists to represent communities of organisms. 
At the moment, there does not seem to be anything like this in Bioperl. 
I am happy to make these modules available under the Bioperl umbrella 
using the Bio::Community::* namespace.

I envision the following modules:
* Bio::Community::Member module representing members of a community.
* Bio::Community::IO modules to read/write files that describe community 
composition (a.k.a. OTU table, or site by species table) as used 
programs like QIIME, Pyrotagger, GAAS, ...
* Bio::Community::Tools modules to help manipulate communities, e.g. to 
take some members at random, normalize the community to a given number 
of individuals, or do rarefaction curves.

The idea is to implement these modules in Moose to teach myself Moose. 
The members of a community could be a sequence (Bio::SeqI), a species 
(Bio::S), an arbitrary string or even other things. I am not quite sure 
if Bioperl provide facilities to attach some arbitrary information to an 

Any interest? Ideas? Comments?



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