[Biopython] Teaching BioPython

[Peter Cock]

On Wed, Jun 22, 2011 at 11:51 AM, Aisling ODriscoll
<Aisling.ODriscoll at cit.ie> wrote:
> Many thanks to all who have taken the time to reply and to provide links and
> advice. Apologies, I should have been more explicit about the course
> duration.
> It will be a 1 hour lecture and 2 hours lab delivered over 11 weeks
> (excluding assessments). I will probably introduce them to a little Perl as
> well (but not too much because otherwide it will just become confusing for
> them I think) so I would imagine at least 8-9 weeks will be dedicated to
> Python/Biopython.

Oh right - so a total of about 11 hours lectures and 22 hours in the lab.
That does make things much more interesting (and more work).

> So I need to devise 8/9 weeks of lecture notes and 8/9 weeks 2 hour lab
> exercises and problems - While the first week or so might be dedicated to
> just getting to grips with Python (they have 4 non contact hours too per
> week so they can use them for this), I want to introduce them to BioPython
> and applying programming to biology-related problems as quickly as possible
> so that they can see the relevance of what they're doing.

I would start by looking at existing introductory Python materials, and probably
put a little more emphasis on string manipulation with biological sequence
examples. Maybe get them to write their own FASTA parser as an exercise,
before then bringing in Biopython.

I've never tried to teach (Bio)python on that scale - but if you find any errors
or omissions in our documentation (especially the Tutorial), we would
welcome feedback.

Peter