[Bioperl-l] Use of Bio namespace

Ewan Birney birney@ebi.ac.uk
Tue, 10 Oct 2000 08:49:42 +0100 (GMT)

On 9 Oct 2000, Keith James wrote:

> Hi all,
> As the current (and a far as I know, sole) occupants of the Bio::
> namespace I thought this would be the forum to ask about any plans for
> namespace organisation of biology-related contributed to CPAN in the
> future.


> The CPAN FAQ suggests nested module names and not making new top-level
> categories unless there is a very good reason, so do people have a
> view on where, say, (non-molecular) biology related stuff should go?
> Or, as in my situation, where non-Bioperl sequence/feature
> etc. modules with similar applications should go to avoid clashes and
> confusion.

I would hope that sequence/feature stuff could be merged inside bioperl
but there

	(a) maybe good reasons not to

	(b) you may not want to ;)

both of which are sensible compliants.

I guess - hmmmmmm - this is hard. I suspect the right thing to do is

	- for really different stuff, eg Ecology, it should get its own
top-level namespace.

	- for similar stuff, people should negoiate a namespace that can
be kept separate for their work, for example, I could imagine


being given out to a separate expression focused group. Bio::TreeOfLife
would be another one. 

	I guess anything molecular biology orientated should end up inside
Bio:: but by no means handled by Bioperl.

I certainly don't want to stop anyone submitting anything to CPAN, so
make a proposal for what you want to submit or how you would best like it

I would also encourage you to 

	- if possible, work with bioperl or criticise bioperl if it wasn't
good enough for what you wanted to do.

	- use the bioperl cvs resources if you want a stable place to
mount a cvs repository etc. Also check out theopenlab.org as another
option for this.

> thanks,
> Keith
> -- 
> -= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
> The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420