[Bioperl-l] BioPerl CPAN

[Nathan (Nat) Goodman]

I agree with Ewan's plan (summarized below) and will make it so.

> that sounds great. What I think we should do is:
>
>   Nat (or someone at ISB...) get a CPAN handle from the CPAN guys....
>  Someone (perhaps in Nat's group...?) needs to learn from Chris Dag/Jason
> where the bioperl web site source code is and how to put up a new page.
>   then submit the code away!

It'll take us a week or so to get organized, and then off we go.  We will
also avail ourselves of Allen Day's offer of help.  I think Aaron Mackey was
interested, too.

> What are the Biblo modules like? Are they very similar or different to the
> ones from Martin Senger in Bioperl

They are based on Martin's existing Biblio framework.  They fit in the same
namespace, use some key pieces of his existing code (esp. XML parsing and
data objects for PubMed references) and attempt to follow his interface
design.  In the end, I was able to implement his interface fairly well for
PubMed but not for some of my other data sources, since the underlying
sources lack some of the capabilities assumed by the interface.

It's checked in under under the branch-1-2-collection tag (freaky-dev).  The
main code is in Bio/DB/Biblio with additional code at Bio/Biblio/IO.  Module
ncbi_eutils is the main guy.  Note that I put my PODs in separate .pod files
since (1) I haven't been able to find an emacs mode that truly understands
embeded POD, and (2) when I'm looking at code, I like to see code, not
documentation.

As a caveat: the code and docs are not quite ready for release.  The docs
need a little cleanup, the code doesn't handle web errors gracefully, and
the tests are not yet in BioPerl 'standard' form.

Best,
Nat