[BioPython] Biopython projects for students

[Brad Chapman]

Hi James;

> > I'm trying to come up with Biopython projects for final year students in
> > my dept. Problem is: I have to define the projects now, but the students
> > don't start on them until October! I'm worried that a project which says
> > "add support for x to BioPython" might be superceded by the time October
> > comes around. If anyone can think of something useful, but which is
> > unlikely to be done that soon, I would appreciate your thoughts.

I think there are a couple of ways to get around this problem. The
one you mention, pick projects that won't be done by October, is a
bit tough due to needing to predict the future. I only wish I could
do that (and only imagine I can when arguing about this year's
predicted Super Bowl winner), so it's tough to give an answer on
that. Another way is to have defined projects that could be more
flexible than just adding a module that does something new.

What I'm thinking here is that projects could be defined more as
"contributing a module considering what Biopython already has."
Okay, I know that doesn't really make a lot of sense so let me try
to explain what I'm thinking with an example. Some modules in
Biopython are pretty complete and do what everyone wants them to do
(BLAST, Fasta...) but some parts do work, but don't do everything
they could. For example (to pick on my own code):

=> Bio.Align and Bio.Clustalw -- deals with Clustalw output and
converting to FASTA format. But, there are also plenty of alignment
formats that still aren't dealt with: phylip, PIR... Similarly there
are a number of alignment programs that aren't supported: T-Coffee,
POA...

=> Bio.Emboss -- all of the Emboss program commandlines are in no
way covered here.

So what I'm suggesting is that the projects could work with the
code-base and add things that are needed -- more formats, more
documentation, more tests (especially tests and docs). This way you
don't have to worry about what gets finished, and things are also
more "real life" since students deal with existing code, programmers
who have done that code, and all of the horrors of writing tests and
the like.

Andy writes:
> I can come up with some ideas..
[...]
> Just some things off the top of my head

Thanks Andy -- these are definitely some good ideas (also, sorry I
didn't find you to say adios from San Diego -- great to see you).
Jeff also listed a few directions in the docs about contributing to
Biopython:

http://www.biopython.org/docs/developer/contrib.html

Hopefully those plus my ranting above helps a bit!
Brad