[Biopython] Teaching BioPython

[Eric Talevich]

On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll <Aisling.ODriscoll at cit.ie
> wrote:

> Hi everyone,
>
> I have been asked to deliver BioPython classes to biologists. Having a
> computer science background myself (Python), I am not finding it easy to
> tie python back to concepts that the biology students will relate to.
> This will be very important as I'm not there to teach them to be expert
> Python computer programmers - they're programming skills must relate to
> their discipline. Has anyone delivered such a course? Even better would
> someone have any lesson plans available which I could use as a starting
> point?
>
> I came across this post but the it's a bit old and the information
> provided in the link no longer seems to be hosted.
> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>
>
Hi Aisling,

I've run a few 2-hour workshops on Python and Biopython at the University of
Georgia using these slide sets:
http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics

I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
can send that to you when it's done if you'd like (or post it here).

The second chapter of the official tutorial, Quick Start, is a good starting
point for designing your own lecture and lab, pulling in more detailed
material from the other chapters as needed.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Also: It's much easier to run a workshop if the participants have set up the
same environment on their own laptops, or the computers on site all have the
same software installed. Specifically, make sure everyone has IDLE and
Python 2.7 installed. Earlier I let students choose between ipython and
IDLE, and during the workshops I typed my examples into ipython -- this was
highly confusing for 100% of the students, including those who did have
ipython installed but weren't familiar with it. In IDLE, everyone has the
same environment and GUI, and the distinction between interpreter and script
is clear.

Cheers,
Eric