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

Hilmar Lapp hlapp at gmx.net
Fri May 15 14:44:50 EDT 2009

On May 15, 2009, at 1:07 PM, Albert Vilella wrote:

> 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.

That should be a positive, no?

I understand that there have been (are?) good reasons for inertia on  
the Ensembl end - undoubtedly such a switch would require a huge  
amount of testing to be sure all the wrinkles have been ironed out. So  
the question I'd like to ask is, from an Ensembl perspective what  
BioPerl features or functions or other things we can actually control  
would make that effort worth it?

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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