Thu, 7 May 1998 09:21:38 -0400
I'm hoping that the NCBI modules will be integrated into the BioPerl
framework, rather than a 1:1 mapping of the NCBI toolkit (although
there will probably be an 1:1 NCBI layer down below). Lewis tells me
that this might not be too hard to accomplish.
Gunther Birznieks writes:
> I would like to add my own personal voice to the enthusiastic noise.
> I am also extremely interested and excited to hear about a perl interface
> to the NCBI Libraries. Some additional comments appear below:
> At 09:13 PM 5/6/98 +0100, Ewan Birney wrote:
> >So - my take on this is that it would be better to make NCBI the root
> >namespace. Reasons -
> > a) NCBI is unique (?) and its inclusion in the Bio:: heirarchy
> >is just for 'documentation' purposes.
> > b) There are things in NCBI (eg ASN stuff) that is not directly
> >anything to do with biology
> > c) (and most importantly) the functionality inside Bio::
> >heirarchy can be assummed to sensibly work together - and the
> >functionality coming out of the NCBI may well work seemlessly with
> >everything else, - but - not for certain. By drawing a valid distinction
> >at the top level between NCBI:: and Bio:: people can understand what
> >they are using and who to expect what from (rather like some collaborative
> >C programming projects where function names start with your initials ;)).
> > I think you'll be confusing more people by trying to present once
> >seemless Bio:: view to people than the necessary 'pick up the following 2
> >module trees - Bio::, NCBI::...
> I think it depends on the intent of this Perl integration and how far this
> will be taken.
> If a strong effort is made to make the NCBI hierarchy meld with other
> modules in the Bio:: hierarchy, I think it should be under Bio:: if possible.
> However, if this is primarily an effort to simply provide a plain vanilla
> 1-to-1 mapping perl interface to the NCBI Toolkit libraries, then I agree
> with the above statement about being less confusing if it is part of its
> own package.
> Anyway, regardless of the hierarchy, I am really excited to hear about this.
> Gunther Birznieks (firstname.lastname@example.org)
Lincoln D. Stein Cold Spring Harbor Laboratory
email@example.com Cold Spring Harbor, NY
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