[Biopython-dev] Moving Bio.Motif documentation into Tutorial.tex

[Peter]

On Tue, Oct 19, 2010 at 1:34 PM, Bartek Wilczynski <barwil at gmail.com> wrote:
> Hi,
>
> I've started to look into merging Bio.Motif docs with the Tutorial. I have a
> few questions:
> - First, I need to find a good place in the tutorial to put it.
>    One possibility is to make a separate chapter for it, another option is
> to put it as a subchapter in chapter 15 (cookbook).
>    I think it would be better to make it a separate chapter, similar to one
> the ones discussing Bio.popgen or bio.phylo, So i thought it would make
> sense to create it as a new chapter 13, entitled Sequence motif analysis
> with Bio.Motif

I agree, create a new chapter (and add yourself to the authors list).
I'd definitely put it before the "Cookbook Chapter", and between the
Phylogenetics and "Supervised learning methods" chapters seems
reasonable.

> -second, I have links and references to papers in there. The question would
> be should I remove those to keep to the style of the tutorial

Keep them - links to external webpages are fine - they work well in both PDF
and HTML. For references we currently don't have a formal bibliography - but
we do have some existing case of links to papers already, e.g.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqIO-fastq-conversion

Peter