Hi David,

These short courses may be of interest:
http://scriptogr.am/ohofmann/intro-to-galaxy

http://scriptogr.am/ohofmann/rna-seq

http://scriptogr.am/ohofmann/exome-seq


Ilya


On 4/25/13 10:11 AM, "David Joly" <idj...@gmail.com> wrote:

>I was pretty much interested in Bio-Linux. However, the version of Galaxy
>that comes with it is already outdated and there is no easy way to update
>it. It is possible to delete it and re-install a newer version, this
>would be another possibility...
>
>Le 2013-04-25 à 05:50, Hans-Rudolf Hotz a écrit :
>
>> 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/Bioinform
>>>aticsTraining
>>> 
>>>    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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>>> 
>>> 
>>> 
>>>    --
>>>    http://galaxyproject.org/GCC2013
>>>    http://galaxyproject.org/
>>>    http://getgalaxy.org/
>>>    http://usegalaxy.org/
>>>    http://wiki.galaxyproject.org/
>>> 
>>> 
>>> 
>>> 
>>> ___________________________________________________________
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>>> 
>
>
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