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

Jason Stajich jason at bioperl.org
Mon Mar 23 12:54:34 EDT 2009

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.

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

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