Teaching using Galaxy

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Teaching using Galaxy

David Joly
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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using "reply all" in your mail client.  For discussion of
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Re: [galaxy-dev] Teaching using Galaxy

Dave Clements-3
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:

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 <[hidden email]> 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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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--
http://galaxyproject.org/GCC2013
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: [galaxy-dev] Teaching using Galaxy

David Joly
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 <[hidden email]>
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:

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 <[hidden email]> 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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/



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


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: [galaxy-dev] Teaching using Galaxy

Dave Clements-3
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

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 <[hidden email]> 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 <[hidden email]>
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:

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 <[hidden email]> 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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/



--
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/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Teaching using Galaxy

Hans-Rudolf Hotz
In reply to this post by David Joly
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 <[hidden email]
> <mailto:[hidden email]>>
>
>     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 <[hidden email]
>     <mailto:[hidden email]>> 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
>
>         ___________________________________________________________
>         Please keep all replies on the list by using "reply all"
>         in your mail client.  To manage your subscriptions to this
>         and other Galaxy lists, please use the interface at:
>         http://lists.bx.psu.edu/
>
>         To search Galaxy mailing lists use the unified search at:
>         http://galaxyproject.org/search/mailinglists/
>
>
>
>
>     --
>     http://galaxyproject.org/GCC2013
>     http://galaxyproject.org/
>     http://getgalaxy.org/
>     http://usegalaxy.org/
>     http://wiki.galaxyproject.org/
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: [galaxy-dev] Teaching using Galaxy

David Joly
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 <[hidden email]
>> <mailto:[hidden email]>>
>>
>>    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 <[hidden email]
>>    <mailto:[hidden email]>> 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
>>
>>        ___________________________________________________________
>>        Please keep all replies on the list by using "reply all"
>>        in your mail client.  To manage your subscriptions to this
>>        and other Galaxy lists, please use the interface at:
>>        http://lists.bx.psu.edu/
>>
>>        To search Galaxy mailing lists use the unified search at:
>>        http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>>
>>    --
>>    http://galaxyproject.org/GCC2013
>>    http://galaxyproject.org/
>>    http://getgalaxy.org/
>>    http://usegalaxy.org/
>>    http://wiki.galaxyproject.org/
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
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