[Bioperl-l] Offering to help

Chris Fields cjfields at illinois.edu
Tue Mar 3 12:14:19 EST 2009


On Mar 3, 2009, at 8:56 AM, Bryan Bishop wrote:

> On Tue, Mar 3, 2009 at 8:34 AM, Chris Fields <cjfields at illinois.edu>  
> wrote:
>> ...
>> For an example of how to get involved with BioPerl search the mail  
>> archives
>> for the recent Bio::DB::HIV work by Mark Jensen, now in BioPerl 1.6.
>
> Neat. I'll have to look into that.
>
>> We would happily support lab protocols if we have a standard to go  
>> by (i.e.
>> schema to work with) and someone willing to code and maintain modules
>
> Have you looked into CLP-ML? I wrote up a pcr.xml example the other
> day, I think I linked to it in my second to last post (maybe). (I'm on
> the run, sorry for not linking at the moment.)

The key issues for inclusion into a stable bioperl release are (1)  
support and (2) stability; we can't have something going to CPAN that  
may have a fluctuating API w/o a decent deprecation cycle.

We can make, however, make the space for in-development modules and  
module API changes (see recent talk of bioperl-dev).  One could:

1) install a stable bioperl release (1.6)
2) optionally install or set PERL5LIB to bioperl-dev (for the bleeding  
edge)

For a Moose-based bioperl implementation I suggest a separate repo  
completely.  We're using svn currently on dev.open-bio.org, though I  
and a few others are also using git.  I'm neutral on the matter but  
it's possible the consensus may be to keep everything in the open-bio  
svn repo (not everyone has git or uses it).

>> related to their use.  As for a place to fit in, we have the various
>> Bio::Biblio modules; I could easily see protocols fitting into that
>> namespace, though I have to admit I'm unfamiliar with the overall
>> structure/purpose of Bio::Biblio.
>
> What? Is that a BibTeX parser module?
>
> - Bryan
> http://heybryan.org/
> 1 512 203 0507

I think Bio::Biblio is the generic class structure for various  
bibliographic sources; the parsers would be in Bio::Biblio::IO (no  
BibTex AFAIK).  They're probably in need of some work.

chris




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