[Bioperl-l] Offering to help
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>
>> For an example of how to get involved with BioPerl search the mail
>> 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
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
> 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.
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