Hi David

I have not used or tested it myself yet, but: have you looked into "Bio-Linux" ?


The latest release (Bio-Linux 7) comes with Galaxy pre-installed, see:

http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info



Regards, Hans-Rudolf


On 04/25/2013 12:52 AM, David Joly wrote:
Thanks Dave!

The focus is clearly more like your second description. The course is
not intended to show them how to use command lines, or how to navigate
in a UNIX environment and how to program. In fact, I think some would
call what I have in mind more of a "computational biology" course than a
"bioinformatics" course, but I think it is not really important here.
I'm thinking of another course to introduce them to the UNIX environment
and using Python to script simple programs, but for this one, I'd prefer
staying away from a terminal that can be horrifying at first (for most
students, black screen = evil)

So, the course is about knowing the tools and their basics, and how to
use them (in this case using Galaxy as the platform). What is a sequence
alignment, why should we do a sequence alignment, how a sequence
alignment work, and how can I do one in Galaxy. This is only one
example, other (and often inter-related) topics would include BLAST,
phylogenetics, sequence polymorphisms, and so on, up to analyzing
next-generation sequencing data...

Regarding how I'll set my environment, I was thinking of setting a local
instance (I have one on my computer right now and I'm already getting
familiar with it). The hardware on which I'll set the instance for the
course is another issue, but this is not the topic of this email...

I'll have a better look at how I could use published histories and
workflows...

Thanks,

DJ


2013/4/24 Dave Clements <cleme...@galaxyproject.org
<mailto:cleme...@galaxyproject.org>>

    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
    <mailto: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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