[Bioperl-l] RE: Bio::FeatureHolderI interface confusion

Hilmar Lapp hlapp at gmx.net
Thu Jun 19 12:28:50 EDT 2003

On Thursday, June 19, 2003, at 05:04  AM, Nathan ((Nat)) Goodman wrote:

> This debate seems to resurface every once in a while.

Hi Nat, yes obviously it does. Not too surprisingly mostly from new 
users ...

I'd really appreciate if Chris' rant and the ensuing debate would lead 
to some tangible action or even results that the different camps are 
both happy or happier with.

>   Perhaps we should
> post a concise summary of the various points somewhere on the website 
> so
> that next time someone raises the concern, he can be pointed there.  
> I’d be
> happy to write up “my” side with the help of Chris Mungall and Steve 
> Mathias
> and anyone else who’d care to contribute.  It wouldn't be much fun, 
> though,
> unless the other sides posted their views, too.

I'll try extract the gist from my postings. There should also be a 
related thread from last fall or so.

>>> There should be a CPAN-like repository…
>> Good suggestion. Volunteers welcome :-)
> Both you and Ewan said the same thing. Good idea if someone would do 
> it.  I’
> ll take the bait.  I'll do it IF the core developers are willing to 
> populate
> it with an initial load of modules.

If you take the lead and lay out the principles along which to 
populate, I'll help filling it with life.

> What I have in mind is moving ‘non-essential’ modules out of the main
> BioPerl distribution and into optional libraries.  There’s probably an 
> 80-20
> rule at work – 80% of BioPerl usage probably involves 20% of the 
> modules.
> The main distribution should have those 20% and the repository should 
> have
> the rest.

I see. So we'd have to draw up a dependency tree.

> This could be phased in over a period of time – say a year.
> I would imagine using the CPAN software – no need to reinvent the 
> wheel!  We
> could call it BPAN or BioPAN or BioCPAN or something.

BioPAN gets my vote. Sounds like a molbio frying pan.

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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