Hi David,

Galaxy does sound like a great match for this course.  It could also play a
(smaller) part in the other course you are considering.  Part of the course
could include installing Galaxy and wrapping other tools to put into it.
 We are a Python based framework

I do strongly recommend you look at http://aws.amazon.com/grants/ for both
courses.  We have been using Amazon in our workshops for a year now and it
has been a big win.

There is also a wealth of material out there on how other people train
using Galaxy.  See

  http://wiki.galaxyproject.org/Events#Past_Events - lots of links to
presentations
  http://wiki.galaxyproject.org/Documents/Presentations - same material,
different order
  http://wiki.galaxyproject.org/Learn - the Galaxy learning hub, especially
  http://wiki.galaxyproject.org/Learn#Other_Tutorials

And, maybe, hopefully, real soon now, there will be a Galaxy "Teaching and
Training" hub page as well (been on my TODO list for a while, but expect
something before GCC2013, really).

Dave C.




On Wed, Apr 24, 2013 at 3:52 PM, David Joly <idj...@gmail.com> 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>
>
>> 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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>>
>>
>>
>> --
>> http://galaxyproject.org/GCC2013
>> http://galaxyproject.org/
>> http://getgalaxy.org/
>> http://usegalaxy.org/
>> http://wiki.galaxyproject.org/
>>
>
>


-- 
http://galaxyproject.org/GCC2013
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
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