[Bioperl-l] BioPerl CPAN

Lincoln Stein lstein at cshl.edu
Thu Jul 17 11:42:37 EDT 2003


I was out of it because of paper writing. What is the upshot of this 
discussion?  Any action plan?


On Wednesday 02 July 2003 09:22 am, Nathan \(Nat\) Goodman wrote:
> Hi Folks
> This is a great discussion.
> Jason & Aaron and Heikki gravitated to the two extremes of what might be
> done with the repository.  The Jason/Aaron thought, in Jason’s words, is
> that this would “be a way for people to get their own code out there sooner
> without it being blessed by 'bioperl'.”  Heikki thought the idea was to
> “split up the current bioperl-live”.
> I think the Jason/Aaron end of the extreme would be extremely valuable in
> its own right. If this is all we accomplish with CPAN it would be worth
> doing, because it would make it easier for the community of BioPerl ‘users’
> to contribute code to the effort even if it isn’t general enough to be part
> of the main BioPerl distribution.
> I think the repository can also be helpful with efforts to simplify the
> existing BioPerl class structure by providing a place to move code that no
> longer fits, or code that just isn’t central enough to warrant a spot in
> the main distribution.  It can also help the BioPerl distribution grow in a
> more coordinated fashion by providing a place for new code to live before
> it gets integrated into the main structure.
> Each of these uses is valuable.  I suggest we test drive the CPAN concept
> with one example of each type.  In other words,
> 1) one contribution that represents code that will probably never migrate
> to the main distribution
> 2) one contribution that represents code from the main distribution that
> needn’t be there
> 3) one contribution that represents code that might migrate to the main
> distribution someday, but isn’t ready for prime time yet.
> I’m happy to volunteer my new Biblio code for type (3).  Some of the
> existing tools stuff could possibly be used for type (2).  I’m sure there’s
> tons of great BioPerl-based code out there that could be used for type (1).
> In terms of the ideas for restructuring the core: my only modest suggestion
> is that it would make sense to defer significant renovations until the
> technical evaluation that’s been discussed recently is carried out.  This
> is to avoid the “ready, shoot, aim” phenomenon.
> Best,
> Nat
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY

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