Hi David,

Using Galaxy to teach undergraduates is a long term interest of mine.
 Which, unfortunately, does not mean I have yet put a lot of thought into
it.  However, lack of thought hasn't stopped me yet.

First, this topic was discussed in a breakout at last year's GCC:

http://wiki.galaxyproject.org/Events/GCC2012/Program/Breakouts/BioinformaticsTraining

That's more of a discussion than a set of best practices.


What do you want them to spend time learning?  Do you want them to learn
the (sometimes grinding) details of using the command line, and how to
install software and their dependencies on a Linux box?  Or do you want to
focus mainly on the high level stuff like here is how and why BLAST works,
and get some practice using it?

I think this question of focus is a central one, and it's one that
well-informed people disagree on.  Galaxy is a great platform for focussing
on the high-level stuff and avoiding the frustration that can come with
installing a C compiler, for example.  On the other hand, if you really
want them to learn the command line, then you might want to start elsewhere.

If you do use Galaxy for teaching, there are a couple of ways you could do
it.  First, I recommend setting up your own server(s) either locally or on
the cloud.  (The AWS in Education grant program is built just for this
case.)  If you wanted to teach them a mixture of high-level and low level,
you could start them out as users on a shared server, and then later in the
course have them setup their own Galaxy on a cloud instance.

Also, for Galaxy training we find that published histories, workflows, and
Galaxy Pages, are a superb way to create exercises.

Hope this helps,

Dave C.



On Mon, Apr 22, 2013 at 12:30 PM, David Joly <idj...@gmail.com> wrote:

> Hi everybody!
>
> I am currently creating a "bioinformatics" course for undergraduate
> (biology students with no knowledge of programming). I would like to use
> Galaxy as their everyday platform where they would learn the basics and use
> the appropriate tools (BLAST and databases, multiple alignment,
> phylogenetics, dealing with "omics" data, and so on).
>
> Is there any available resources about using Galaxy for teaching
> (undergraduates)?
>
> Any suggestions of good textbooks? Not a Galaxy textbook of course, but a
> "bioinformatics textbook" that would be a good companion to help the
> students understand the basics behind the tools.
>
> Thanks,
>
> DJ
>
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