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

[Mark A. Jensen]

Great, this is starting to sound useful-- I'll dig in to the libsequence api a 
bit.
Are you into being a co-mentor for this, or maybe even Kev?
----- Original Message ----- 
From: "Jason Stajich" <jason at bioperl.org>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Chris Fields" <cjfields at illinois.edu>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>
Sent: Monday, March 23, 2009 3:31 PM
Subject: Re: [Bioperl-l] Summer of Code project idea: build-out of 
PopGen::Simulation::Coalescent


> 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
>
>
>
>
>