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

Albert Vilella avilella at gmail.com
Fri May 15 13:07:43 EDT 2009

Heh, I understand what you say. I am in a similar position from the point
that I would prefer to switch to a more modern bioperl but the ensembl
comparative genomics code -- ensembl-compara -- relies on the ensembl-core
code, which relies on bioperl 1.2.3. We could all switch to bioperl 1.6 but
I cannot switch the ensembl-compara code if code doesn't switch as well. I
haven't been very successful in raising this issue so far, but I can try
again :-p

One of the things that has changed a lot is swissprot support (swiss.pm).
Another object that I am using a lot is SimpleAlign.pm, which in the modern
version has a lot more methods.

On Thu, May 14, 2009 at 3:16 PM, 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 on list (here or ensembl) about bioperl versions 5+ years out-of-date?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
>>>> _______________________________________________
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>>> Jason Stajich
>>> jason at bioperl.org
>>> _______________________________________________
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