[Bioperl-l] Google Summer of Code student Chase Miller

[Chris Fields]

Welcome to the BioPerl community Chase!  Let us know if you need any  
help.

chris

(less cranky now I've had my coffee)

On May 14, 2009, at 12:15 PM, Chase Miller wrote:

> Hi all,
> Thanks for the warm welcome.  I'm really looking forward to working  
> with
> everyone.
>
> Albert, I don't have a blog yet.  Currently, you can check the  
> project page
> for any updates (
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:BioPerl_integration_of_the_NeXML_exchange_standard_and_Bio::Phylo_toolkit
> ).
>
> Chase
>
> On Thu, May 14, 2009 at 10:16 AM, Chris Fields  
> <cjfields at illinois.edu>wrote:
>
>> Albert,
>>
>> Just to note, I have been using bioperl 1.6.0 with the ensembl API  
>> w/o
>> problems, and Sendu Bala added an ensembl 'wrapper' to bioperl- 
>> run.  Do we
>> know precisely what breaks btwn 1.2.3 and 1.6 (and thus leads  
>> everyone to
>> believe 1.2.3 is absolutely required)?  The previous answers have  
>> been
>> pretty nebulous and unspecific.
>>
>> I would have to go on record as being opposed to this.  If there is  
>> a true
>> compatibility issue, I would much rather spend the energy and tuits  
>> driving
>> towards ensembl compatibility with the current bioperl version than
>> backporting to 1.2.3.  What about having users popping in with bug  
>> reports
>> on list (here or ensembl) about bioperl versions 5+ years out-of- 
>> date?
>> Furthermore, it's a slippery slope; the next thing will be requests  
>> to
>> backport specific bug fixes in the current branch to 1.2.3.
>>
>> Who's willing to maintain that branch?  We have few devs as it is,  
>> so is
>> someone on the ensembl end willing to take that up?
>>
>> Perl 5 development has been held up with the same issues, something  
>> they
>> have recently just started digging themselves out of.  Regardless,  
>> I think
>> way too many changes have occurred in that particular code that  
>> make such
>> endeavors unrealistic, unfeasible, and unmaintainable.
>>
>> chris
>>
>>
>> On May 14, 2009, at 8:45 AM, Albert Vilella wrote:
>>
>> Hi all,
>>>
>>> In Ensembl, we are interested in providing NeXML dumps for our  
>>> Comparative
>>> Genomics data. Because our pipeline is
>>> written in Perl, I guess most of the work done here will be of  
>>> great use
>>> to
>>> us.
>>>
>>> If I could only ask for only a feature, that would be to *try* and
>>> backport
>>> the NeXML support to bioperl-1.2.3 --- stress on the *try*.  
>>> Bioperl 1.2.3
>>> is
>>> the release that Ensembl decided to stick to many years ago, so it's
>>> cleaner
>>> for people to use our Perl API with only one version of bioperl as a
>>> dependency.
>>>
>>> Looking forward to hearing from this SoC. Have you got a blog?
>>>
>>> Cheers,
>>>
>>>  Albert.
>>>
>>>
>>> On Mon, May 11, 2009 at 5:24 PM, Jason Stajich <jason at bioperl.org>  
>>> wrote:
>>>
>>> Welcome Chase.
>>>>
>>>> Look forward to the project and helping where needed.
>>>>
>>>> -jason
>>>>
>>>>
>>>> On May 11, 2009, at 7:31 AM, Mark A. Jensen wrote:
>>>>
>>>> Hello all,
>>>>
>>>>> With great pleasure, I want to introduce Chase Miller, my Google  
>>>>> Summer
>>>>> of
>>>>> Code student from George Washington University, to the  
>>>>> community. Chase
>>>>> will
>>>>> be working with me and Rutger Vos on a BioPerl wrapper for  
>>>>> Rutger's
>>>>> Bio::Phylo package, with a particular emphasis on creating a
>>>>> BioPerl-native
>>>>> way to import and export the NeXML (http://nexml.org)  
>>>>> phylogenetic data
>>>>> format. He wrote a great proposal, available here:
>>>>>
>>>>> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:BioPerl_integration_of_the_NeXML_exchange_standard_and_Bio::Phylo_toolkit
>>>>> .
>>>>> We will be working throughout the summer on the project, and  
>>>>> will of
>>>>> course come to you for sage advice. I know you will welcome him  
>>>>> warmly,
>>>>> as
>>>>> you did me.
>>>>> Cheers,
>>>>> 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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>>>>
>>>> _______________________________________________
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>>>
>>
>>
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