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

[Mark A. Jensen]

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
>>
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>
> Jason Stajich
> jason at bioperl.org
>
>
>
>
>