[Biopython-dev] Bio.MarkovModel; Bio.Popgen, Bio.PDB documentation

[Peter]

On Mon, Oct 6, 2008 at 11:13 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> > When I was looking at the NumPy-dependent modules, I
>> > got the impression that Bio.MarkovModel can be
>> > simplified now that it's using the new NumPy.
>>
>> That's good, but of limited benefit in itself.
>
> Well, currently Bio.MarkovModel uses a C extension module
> Bio.cMarkovModel. If we can achieve the same speed or better
> by making use of NumPy, then we won't need this C extension
> module and we can simplify Biopython.

I'd missed the C extension module - yes, if we can drop that by making
more use of numpy this does sound worth while.

>> > 2) If not, should this module be kept?
>>
>> I would say yes.
>> ...
>> To me, having this remain as a "top level" module in
>> Biopython would give it higher status and visibility than
>> hiding it away in the example scripts.
>
> OK, let's keep it as a module then. We now have several small
> modules related to supervised learning as separate Bio.<module>s
> (LogisticRegression, MaxEntropy, kNN, NaiveBayes, and arguably
> MarkovModel), which to me looks a bit messy. It may be a good
> idea to collect these in one Bio.Supervised, though this is not urgent.
>
> I'd be happy to set up a new chapter in the tutorial about these
> supervised learning modules (I wrote a section a long time ago
> for the cookbook about logistic regression).

http://biopython.org/DIST/docs/cookbook/LogisticRegression.html
Using that as a basic for a whole chapter sounds excellent.

> While we're on the subject, I think that the Bio.PopGen and
> Bio.PDB sections of the cookbook chapter in the tutorial should
> be promoted to separate chapters in the tutorial, since these
> modules are fairly big and have a good documentation.

Bio.PDB also has a whole separate document, but I am not sure off hand
how much this overlaps.
http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf

I agree that those two sections could be promoted to chapters.  Would
we want to stick with a global authorship? If so Tiago should be
listed for the PopGen chapter.  Alternatively, we could list authors
for each chapter (which will take a little leg work up front) and a
few "editors" (which may well change over time).

Peter