[BioRuby] GSoC speciation/duplication inference question

[Sara Rayburn]

Hi,

I think between the list response and conversations with my mentor, I would probably go with 
Bio::Algorithm::SDI, with the files in lib/bio/util/phylogeny/SDI/

I can definitely see the others as good possibilities, though. If anyone objects to this naming, please let me know so I can change it.

Thanks,

Sara Rayburn
sararayburn at gmail.com 

On Jun 15, 2010, at 9:06 PM, Toshiaki Katayama wrote:

> Hi,
> 
> Replying personally as I delayed to find this thread.
> 
> I prefer something like lib/bio/phylo/sdi.rb and Bio::Phylo::SDI, how about to gather other phyloinformatics modules under the same directory as well?
> 
> Toshiaki
> 
> 
> On 2010/06/10, at 22:46, Naohisa GOTO wrote:
> 
>> 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
>> 
>> 
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>