[Bioperl-l] Interest in Bio::Community modules
florent.angly at gmail.com
Sun Nov 27 23:35:31 EST 2011
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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