[Bioperl-l] Summer of Code project idea: build-out of PopGen::Simulation::Coalescent

[Jason Stajich]

yeah - I've talked to Kevin about some wrappers for the libsequence  
code at one point so it seems like just the thing a SoC could work  
towards.  To some extent there is a reasonable matching of the popgen  
objects in bioperl to the libsequence code, but it may require some  
effort to match well enough.  I think it would make for a great  
project to tie these our object set more closely to it -- If that  
means the bioperl objects have to change, I have no problem with that.  
Right now we are quite inefficient when storing all the markers so it  
can be too slow to read in a whole genome's worth of marker data, but  
with some simpler approaches we can get there.

Will try and weigh in more on the proposals but I think this would be  
a really great project at any level it is addressed.

-jason

On Mar 23, 2009, at 12:09 PM, Mark A. Jensen wrote:

> This is excellent-- I trust all those brains implicitly (looks like
> my entire grad school cohort wrote code for it).
> cheers
> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: "Jason Stajich" <jason at bioperl.org>; "BioPerl List" <bioperl-l at lists.open-bio.org 
> >
> Sent: Monday, March 23, 2009 2:49 PM
> Subject: Re: [Bioperl-l] Summer of Code project idea: build-out of  
> PopGen::Simulation::Coalescent
>
>
>> It might be worth coordinating some of this with BioLib if there is  
>> a  C- or C++-based library around one can link into (in this case  
>> via  swig, not XS). libsequence is supposed to be capable of  
>> coalescence  simulation and has some C code:
>>
>> http://molpopgen.org/software/libsequence/doc/html/index.html
>>
>> chris
>>
>> On Mar 23, 2009, at 1:27 PM, Mark A. Jensen wrote:
>>
>>> Absolutely-- an XS implementation of the guts (at least) is one of
>>> the overall goals. I'm still new to the C <->Perl world, so links to
>>> info in that direction would be very much appreciated-
>>> cheers MAJ
>>> ----- Original Message ----- From: "Jason Stajich" <jason at bioperl.org 
>>> >
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
>>> Sent: Monday, March 23, 2009 12:54 PM
>>> Subject: Re: [Bioperl-l] Summer of Code project idea: build-out of  
>>> PopGen::Simulation::Coalescent
>>>
>>>
>>>> No apologies necessary, this is open source so I am delighted to   
>>>> have others work on this. You might want to recognize that the   
>>>> Perl implementation is slow relative to the C code so at some   
>>>> point for practical utility we may want to also explore an   
>>>> Inline::C component.
>>>>
>>>> -jason
>>>> On Mar 23, 2009, at 6:45 AM, Mark A. Jensen wrote:
>>>>
>>>>> Hi  all--
>>>>>
>>>>> With apologies to Jason, I took the liberty of throwing out an
>>>>> idea or two re the BioPerl coalescent implementation
>>>>> as a NESCent Summer of Code project. The underlying
>>>>> motivation is to make the module more immediately useful
>>>>> to infectious disease evolutionists, and also to lay a foundation
>>>>> for a coalescent API (and who couldn't use another coalescent
>>>>> API?). The main conceptual addition would
>>>>> be writing routines to implement the so-called serial coalescent,
>>>>> which is a natural modification of Hudson's algorithm that
>>>>> allows for specification of the time of the sample, as well
>>>>> as the size and mutation rate.
>>>>>
>>>>> Rather than reproducing the entire screed, I direct interested
>>>>> folks to the following
>>>>>
>>>>> https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 
>>>>>   
>>>>> #Building_out_BioPerl_PopGen 
>>>>>  ::Simulation_modules_for_infectious_disease
>>>>>
>>>>> If this is interesting to you (as a student or as a co- 
>>>>> mentor),   please reply here,
>>>>> respond in the phylosoc at nescent.org list, or contact me directly.
>>>>>
>>>>> cheers all-
>>>>> Mark
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Jason Stajich
>>>> jason at bioperl.org
>>>>
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>

Jason Stajich
jason at bioperl.org