[Bioperl-l] 0.7 release: tasks & assignments

[Ewan Birney]

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
challenge]

> 
> 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
idea.

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
genbank

(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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