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

[Chris Fields]

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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