[Bioperl-l] 0.7 release: tasks & assignments

Ewan Birney birney@ebi.ac.uk
Fri, 1 Dec 2000 08:21:06 +0000 (GMT)

On Thu, 30 Nov 2000, Hilmar Lapp wrote:

[To second hilmar's comment - yup - this is perhaps *the* most important
job for this release/branch cycle and it is great to see you taking up the

> Ewan probably has made rich experience with questions and problems users
> have, as they also held another bioperl-workshop this summer over at
> EBI, where expecially documentation issues arose. So, Ewan, what's your
> point of view?

Cookbook syle documentation, with explanation seems to be the best way for
people to learn the package. Concept documentation (this object inheriets
from this and abstracts the idea of a sequence yadadada) seems to be a bad

Here is some ideas for the quick "cookbook" scripts to write down

(a) calculate average length of sequences in a fasta file

(b) convert EMBL format files to GenBank

(c) take a file of identifiers, retrieve sequences via genbank

(d) take sequence, run blast, put sequence features onto sequnece, dump as

(e) take sequence, run HMMER... you get the idea ;)

(f) index a fasta file for lookup

(g) run gene prediction programs

I think just some these written down will really help people get aquainted
to the package. The code developers can also ensure that this
functionality works smoothly (jason/hilmar - notice the sequence features
on blast have to come out in genbank/embl format. Does not work with
Bio::Tools::BLAST - probably does with BPLite)

> And: folks on the list, this is the time to mail your special mad
> documentation encounter in bioperl to Brian.
> 	Hilmar
> -- 
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> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420