XML vs AnnotationCollectionI [was Re: [Bioperl-l]
AnnotationCollectionI and SeqFeatureI changes]
Aaron J. Mackey
amackey at pcbi.upenn.edu
Wed Nov 24 08:55:42 EST 2004
I think this is a grand idea for what I've called BioPerl "nouveau", in
which we may use any and all existing technologies at our disposal,
regardless of how convoluted and difficult the installation may be,
runtime-instantiated methods (even classes) are allowed, and where we
only care marginally about backwards compatibility, and instead focus
on doing it "right" (of course there are large arguments about this).
In the "nouveau" project, interfaces are hidden from the naive
end-user, documentation is highly structured (and inheritable), parsing
is block- and event-based, and there are flexible API "adaptors" to
provide ultra-simple, light-weight or heavy-weight access to underlying
objects. Sounds great, but still a pipe-dream, unfortunately.
I've been (slowly) writing some use cases for bioperl-nouveau which are
really just example end-user code making use of simple, light-weight
and heavy-weight APIs. Since this is still just a hobby for me, I
haven't made them public yet; is there enough interest (yet) to talk
about what a next-generation BioPerl might look like?
P.S. But Chris, if you actually wanted to get some real work done,
you're welcome to just make a branch and go crazy ... whether we end up
using it in the existing BioPerl depends on whether it ends up being
more useful than the current implementation, and whether the audience
seems willing to install XML tools for such a "core" functionality.
On Nov 23, 2004, at 10:24 PM, Chris Mungall wrote:
> I may play around with something like this on a clean branch if there's
> anyone else who doesn't think this is a mad idea and may actually use
> final results....
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania email: amackey at pcbi.upenn.edu
415 S. University Avenue office: 215-898-1205
Philadelphia, PA 19104-6017 fax: 215-746-6697
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