Bioperl-guts: The BioPerl Cookbook: some thoughts/questions

Ewan Birney birney@sanger.ac.uk
Mon, 30 Aug 1999 18:10:46 +0100 (BST)


On Mon, 30 Aug 1999, Aaron J Mackey wrote:


I think this is sooo cool. Great stuff guys...

> 
> On Mon, 30 Aug 1999, Kris Boulez wrote:
> 
> > - What is the intended audience for such a BioPerl Cookbook (BPC)? Do we 
> > expect the people readin this to have a no/limited/average/advanced/...
> > level of Perl (or programming in general)? 
> 
> The Perl Cookbook starts simple and get's harder - often the recipes
> contain multiple solutions, of increasing complexity.  I think in general
> we are aiming at the limited/average group.

I think we grow this thing from limited to expert. My best ever
programming book was ANSI C which went from hello world to memory
management system in under 10 chapters. A great book...

>
> Yes, but in some sense that's what each module's pod documentation should
> accomplish (in conjunction with the introductory information in
> bioperl.pod)
>

In general I think there should be a way of keeping the cookbook in
perfect sync with the documentation. Kris - I am not sure what you are
considering for the format of the cookbook but if it is latex or docbook
or someother structured language, it should be ok to write a pod2 (or
more properely a bioperlpod2 as we have our own function definitions 
inside pod) to the format. This might mean some internal changes to our
documentation, but that would be a good thing...

One key thing for me is that it is *readable* in the sense that an Oreilly
book is readable. (you can print it out, etc, etc). This is more than 
pod or html pages.

 
> > - Should the BPC contain a (short) introduction to OO (see also the
> >   first question)?
> 
> Perhaps, but definitely short with pointers to existing Perl resources on
> learning/using modules.
> 
> > - I see the BPC as a replacement/extension/... of what is now in
> >   scripts/ and examples/ . Any comments?
> 
> Certainly, the BPC should incorporate and extend valuable code in scripts/
> and examples/, and all the full recipes in BPC should coexist in
> examples/.

seconded

> 
> > _ Does someone has a (good) idea for a real world problem that could be
> > included in the BPC?


Aaron's examples look good. I'd just start pitching in Kris. Whatever you
do will be great I am sure! This will make a BIG difference to the
project. (I am pretty sure in writing the book you will find some key
yhings we have left out/not done correctly etc...).

[snip]

Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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