[BioRuby] GSoC speciation/duplication inference question

[Naohisa GOTO]

Hi,

I think the abbreviation SDI is not common in the field of biology
and bioinformatics. In this case, it is generally good not to
abbreviate, but the "speciation/duplication inference" is too long.
For file/directory names, because the length limit is tight,
using abbreviation is good.

For the location of files, I suggest
lib/bio/util/evolution/SDI/ or lib/bio/util/phylogeny/SDI/
to show the word SDI is in the field of evolution or phylogeny.

For the class/module namespace,  possible candidates are
Bio::SpeciationDuplicationInference, Bio::Evolution::SDI,
Bio::Algorithm::SDI, but I couldn't determine which is the best.
If you have good idea, please tell us.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


On Mon, 7 Jun 2010 13:09:07 -0500
Sara Rayburn <sararayburn at gmail.com> wrote:

> Hello,
> 
> While implementing my gsoc project (the speciation/duplicaiton inference algorithm), I'm not sure where to put the module I'm developing in the bioruby library. I've been developing in the lib/bio/util directory, but I want to make sure that's the place you all would prefer for the module. Any suggestions or thoughts?
> 
> Thanks,
> 
> Sara Rayburn
> sararayburn at gmail.com