[Biopython] Teaching BioPython

[Aisling ODriscoll]

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.
 
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. 
 
Kind Regards,
Aisling.

________________________________

From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
Sent: Wed 22/06/2011 08:46
To: Eric Talevich
Cc: Aisling ODriscoll; biopython at lists.open-bio.org
Subject: Re: [Biopython] Teaching BioPython



On Wed, Jun 22, 2011 at 1:29 AM, Eric Talevich wrote:
> 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

Certainly that could be a good basis - but you're going to have to
be selective given the limited contact time. Realistically you can
expect the students to type in and run some short examples, and
get a flavour of Python (and Biopython). For most of them that
will be all the take away - but a few could be tempted to learn more
(of Python or programming in general).

> 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.

For a short course like yours, this is essential - otherwise you (Aisling)
could easily spend the first hour troubleshooting several different setups
and making sure everyone can start the examples.

> 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.

Assuming your class are not using the Mac, I'd also use IDLE in a class.
Apple doesn't include it by default on the Mac for some reason.

It is likely your group be using a set of Windows machines, so the
installation of Python 2.7, NumPy and Biopython via the installers
should be easy. You might also look at the Enthought Python Distribution,
which I think comes with them all bundled (but not necessarily the latest
versions).

Peter