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

[Mark A. Jensen]

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
>>>
>>>
>>>
>>>
>>
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>
>
>