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

Bartek Wilczynski barwil at gmail.com
Tue Oct 19 12:34:45 UTC 2010


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
-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

any thoughts are welcome


On Sat, Sep 18, 2010 at 3:04 PM, Bartek Wilczynski <barwil at gmail.com> wrote:

> Hi,
> On Sat, Sep 18, 2010 at 2:25 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>> Hi Bartek,
>> I think it would be good to try and move your Bio.Motif
>> documentation from file Docs/cookbook/motif/motif.tex
>> into the main Docs/Tutorial.tex as a new chapter.
>> Currently it isn't obvious that Biopython supports
>> things like a Position Weight Matrix (PWM).
>> What do you think?
>> The text will need a slight update since we have now
>> deprecated and removed Bio.AlignAce and Bio.MEME,
>> but that should be easy.
> In general, I'm all for it. It's just that right now is not necessarily the
> best time for me to put much work into it. I'm trying to meet a RECOMB
> deadline of Oct. 8th with a paper, so if it would not be a problem, I could
> update it to the current state of the API after that. On the other hand, if
> there's anybody who wants to do it before then, I can review the changes
> even earlier.
> thanks for remembering about it.
> Bartek

Bartek Wilczynski
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
tel: +49 6221 387 8433

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