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

Chris Fields cjfields at illinois.edu
Thu May 14 10:16:46 EDT 2009


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years out-of-date?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  


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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list