Re: [Discuss] inverted carpentries?

[David Martin (Staff)]

I make extensive use of videos in the courses I teach. I find the carpentries 
method to be not suitable for novices (ie the starting from scratch group)  for 
the reasons given - there is no context on which to hang the material they are 
given. The videos typically will be taking them through the introduction parts 
- what is a list, how do you work with it etc.) and they then have exercises 
('labs') in iPython notebooks. They make extensive use of the videos for 
reference during their labs which typically are started in class and then 
homework to be worked through during the week.


This is mid undergraduate (Scottish level 2 and 3, level 4 is honours). 
Postgrads are typically selected as being more able students so they are better 
able to handle the intensity and use scaffolding better.


I like the carpentries approach but it is not suitable for all cases, and I 
also like to see these developments springing up from it. The benefit of 
carpentries is that they give the students two things - the knowledge that a 
certain thing can be done, and the knowledge and confidence that it is within 
their ability. These allow/permit/encourage a student to then take the further 
steps in learning as they need to.


..d


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee


From: Discuss  on behalf of Ethan 
White 
Sent: 16 March 2018 15:28:30
To: Greg Wilson; Software Carpentry Discussion
Subject: Re: [Discuss] inverted carpentries?

I think this is a really interesting idea and I tried this a few years back in 
the university classroom in my Carpentries' style courses (i.e., 
https://www.programmingforbiologists.org/ & 
http://www.datacarpentry.org/semester-biology/). I found that the classic 
approach of watching videos in advance and then jumping straight into exercises 
in class was great for the top 20% of students. They had basically processed 
things successfully on the first exposure (the videos) and enjoyed getting to 
immediately apply it. It did not work as well for the bottom 50% of students. 
Watching the videos had given them a useful first exposure, but lacking the 
well developed scaffolding to hang that information on it had already started 
to fade and they couldn't immediately apply it. They wouldn't speak up about 
not getting it quickly enough and would struggle.

As a result I ended up switching to teaching my university classes on this just 
like we teach workshops, but with just a little more assumption of having seen 
the basic idea before in readings/videos. Students view the material in 
advance. I then provide a brief overview of the first topic and show one or two 
examples. The students then work on an example that builds on what I just 
demonstrated and we iterate this way throughout the class period. This feels a 
little slower to the top 20% of students, but I've found it to be more 
effective for everyone else.

This is also in a fairly ideal setting for this kind of approach in that the 
students are graded so there is external pressure to come prepared and the 
exercises we do in class count towards their grades. All of this is to say that 
based on my (certainly limited) experience doing things both ways in the 
university classroom that the I do, we do, you do, style of the current 
workshops may end up being the best approach.

That said experimentation is always good and I like Greg's idea of a fusion as 
a possible approach to letting students move at different speeds and 
potentially learn different material. We should just pay attention to make sure 
that this doesn't end up leaving the folks behind that need us the most.

Ethan

On 03/14/2018 07:39 AM, Greg Wilson wrote:

I like the idea of flipping the Carpentry classroom as well, but I think the 
first day or two should still use our regular approach: for many learners, the 
biggest benefit of a workshop is the way it helps them get over the FUD (fear, 
uncertainty, and doubt) they feel whenever they try to get computers to be 
useful, and I don't think that starting with videos will accomplish that.

An experiment I'd really like to try is a regular two-day workshop immediately 
followed by the same people working side-by-side in the same classroom through 
a series of video lessons, with the helpers still there to assist them whenever 
they hit a stumbling block. Different learners could go at different speeds, or 
even through (somewhat) different material, but they would still get the social 
benefits of working alongside their peers, and the instructional benefits of 
one-to-one assistance when most needed. I haven't been able to find anything in 
the educational research literature describing this hybrid model, but I'd be 
willing to bet a dollar that it would outperform either of the pure 
alternatives, and I believe that at least some learners would be willing to 

Re: [Discuss] Code Phonology - on reading code aloud

[David Martin (Staff)]

Those are speech marks. Or as those who have had code mangled by Word put it 
'*expletive deleted* special characters'.

Yes it is a Britishism, but rather archaic in use in the motherland.


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Amy E. Hodge <amyho...@stanford.edu>
Sent: 16 March 2018 23:02
To: David Martin (Staff); Rayna Harris
Cc: Software Carpentry Discussion
Subject: Re: [Discuss] Code Phonology - on reading code aloud


Quotes referred to as “inverted commas” – I’m not sure if this applies to both 
‘ and “, but I heard it for the first time last fall in South Africa.



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194

[cid:image001.png@01D3BD40.1EF8E120] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of 
"David Martin (Staff)" <d.m.a.mar...@dundee.ac.uk>
Date: Friday, March 16, 2018 at 3:46 PM
To: Rayna Harris <rayna.har...@gmail.com>
Cc: Software Carpentry Discussion <discuss@lists.software-carpentry.org>
Subject: Re: [Discuss] Code Phonology - on reading code aloud



Add

^ caret, hat, upside down v

> greater than, right angle bracket (context dependent)

< less than, left angle bracket (context dependent)

' quote

" double quote

'' double quotes 



Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee





From: Rayna Harris <rayna.har...@gmail.com>
Sent: 16 March 2018 22:32
To: David Martin (Staff)
Cc: Madeleine Bonsma; Kevin Vilbig; Software Carpentry Discussion
Subject: Re: [Discuss] Code Phonology - on reading code aloud



Thanks David!



You inspired me to create a table of code 
phonology<https://github.com/Carpentries-ES/board/blob/96e94a023e52e4213775101e624004dc6e35c228/Convenciones_Traduccion.md#fonolog%C3%ADa-del-c%C3%B3digo---c%C3%B3mo-leerlo-en-voz-alta>
 for the Spanish Unix and GIt lessons!



I got most of the data from this ASCII site<http://www.elcodigoascii.com.ar/> 
and from the translated lessons themselves. I agree with Madeleine that it 
would be interesting to see what words our instructors from around the world 
use.



Rayna


Rayna Harris

@raynamharris<https://twitter.com/raynamharris>

http://raynamharris.github.io/



On Fri, Mar 16, 2018 at 6:41 PM, David Martin (Staff) 
<d.m.a.mar...@dundee.ac.uk<mailto:d.m.a.mar...@dundee.ac.uk>> wrote:





From an ENglish point of view..



On Mon, Mar 12, 2018 at 12:14 PM, Kevin Vilbig 
<kvil...@gmail.com<mailto:kvil...@gmail.com>> wrote:

This issue has been on my mind since teaching my first few classes.

Here is a quick lexicon beyond what you mentioned.

{ }  can also be called curly braces

curly brackets, braces

() parentheses, round brackets

[] brackets, square brackets

! can be called bang or exclamation point

exclamation mark, pling

# can be called crunch, sha, pound, or hash

Typically hash
\ backslash or backwhack
/ slack or whack

forward slash or divide
* star or wildcard or asterisk
~ tilde or that wiggly line next to the one key

squiggle (next to RETURN, ENTER in UK)

_ underline, underscore

- dash, hyphen

. full stop, dot

` backtick, no not quote, the other one.


And that's only for single characters! What about compound character operators? 
Perl 6 can even take some unicode symbols as arithmetic operators!



On Mon, Mar 12, 2018 at 10:40 AM, Amy E. Hodge 
<amyho...@stanford.edu<mailto:amyho...@stanford.edu>> wrote:

I found this very interesting. I also find that mixtures of cultural 
backgrounds in the class – or a difference between myself and the learners – 
can sometimes lead to confusion in the different ways people describe the 
symbols in particular.



I spent the first half day leading a week-long training (not for coding, but 
for something internal to the company I was working for where there was an 
internal “language” to be learned) before I realized that while I was 
describing them as “braces,” “square brackets,” and “parentheses,” my learners 
described these as “flower brackets,” “square brackets,” and “round brackets,” 
and the three together under the umbrella of “brackets,” which I only used in 
reference to the square ones. Learning got much faster after we got that 
squared away!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194<tel:(650)%20556-5194>

[cid:image002.png@01D3BD40.1EF8E120] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services

Re: [Discuss] Code Phonology - on reading code aloud

[David Martin (Staff)]

Add

^ caret, hat, upside down v

> greater than, right angle bracket (context dependent)

< less than, left angle bracket (context dependent)

' quote

" double quote

'' double quotes 


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Rayna Harris <rayna.har...@gmail.com>
Sent: 16 March 2018 22:32
To: David Martin (Staff)
Cc: Madeleine Bonsma; Kevin Vilbig; Software Carpentry Discussion
Subject: Re: [Discuss] Code Phonology - on reading code aloud

Thanks David!

You inspired me to create a table of code 
phonology<https://github.com/Carpentries-ES/board/blob/96e94a023e52e4213775101e624004dc6e35c228/Convenciones_Traduccion.md#fonolog%C3%ADa-del-c%C3%B3digo---c%C3%B3mo-leerlo-en-voz-alta>
 for the Spanish Unix and GIt lessons!

I got most of the data from this ASCII site<http://www.elcodigoascii.com.ar/> 
and from the translated lessons themselves. I agree with Madeleine that it 
would be interesting to see what words our instructors from around the world 
use.

Rayna

Rayna Harris
@raynamharris<https://twitter.com/raynamharris>
http://raynamharris.github.io/

On Fri, Mar 16, 2018 at 6:41 PM, David Martin (Staff) 
<d.m.a.mar...@dundee.ac.uk<mailto:d.m.a.mar...@dundee.ac.uk>> wrote:



From an ENglish point of view..

On Mon, Mar 12, 2018 at 12:14 PM, Kevin Vilbig 
<kvil...@gmail.com<mailto:kvil...@gmail.com>> wrote:
This issue has been on my mind since teaching my first few classes.

Here is a quick lexicon beyond what you mentioned.

{ }  can also be called curly braces
curly brackets, braces
() parentheses, round brackets
[] brackets, square brackets
! can be called bang or exclamation point
exclamation mark, pling
# can be called crunch, sha, pound, or hash
Typically hash
\ backslash or backwhack
/ slack or whack
forward slash or divide
* star or wildcard or asterisk
~ tilde or that wiggly line next to the one key
squiggle (next to RETURN, ENTER in UK)
_ underline, underscore
- dash, hyphen
. full stop, dot
` backtick, no not quote, the other one.


And that's only for single characters! What about compound character operators? 
Perl 6 can even take some unicode symbols as arithmetic operators!

On Mon, Mar 12, 2018 at 10:40 AM, Amy E. Hodge 
<amyho...@stanford.edu<mailto:amyho...@stanford.edu>> wrote:

I found this very interesting. I also find that mixtures of cultural 
backgrounds in the class – or a difference between myself and the learners – 
can sometimes lead to confusion in the different ways people describe the 
symbols in particular.



I spent the first half day leading a week-long training (not for coding, but 
for something internal to the company I was working for where there was an 
internal “language” to be learned) before I realized that while I was 
describing them as “braces,” “square brackets,” and “parentheses,” my learners 
described these as “flower brackets,” “square brackets,” and “round brackets,” 
and the three together under the umbrella of “brackets,” which I only used in 
reference to the square ones. Learning got much faster after we got that 
squared away!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194<tel:(650)%20556-5194>

[cid:image001.png@01D3B9DD.C20D7850] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: Discuss 
<discuss-boun...@lists.software-carpentry.org<mailto:discuss-boun...@lists.software-carpentry.org>>
 on behalf of Lex Nederbragt 
<lex.nederbr...@ibv.uio.no<mailto:lex.nederbr...@ibv.uio.no>>
Date: Monday, March 12, 2018 at 2:48 AM
To: Software Carpentry Discussion 
<discuss@lists.software-carpentry.org<mailto:discuss@lists.software-carpentry.org>>
Subject: [Discuss] Code Phonology - on reading code aloud



Hi,



Felienne Hermans has a really interesting blog post and accompanying paper on 
Code Phonology, i.e. on reading code aloud: 
http://www.felienne.com/archives/5947.



This is relevant for teaching through ‘live follow-along coding’: are we aware 
what vocabulary we use and what effect that has on our learners (e.g. cognitive 
load)? Do we use consistent vocabulary across lessons and between workshops?



Food for thought...



Lex



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--
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Re: [Discuss] Code Phonology - on reading code aloud

[David Martin (Staff)]

>From an ENglish point of view..

On Mon, Mar 12, 2018 at 12:14 PM, Kevin Vilbig 
> wrote:
This issue has been on my mind since teaching my first few classes.

Here is a quick lexicon beyond what you mentioned.

{ }  can also be called curly braces
curly brackets, braces
() parentheses, round brackets
[] brackets, square brackets
! can be called bang or exclamation point
exclamation mark, pling
# can be called crunch, sha, pound, or hash
Typically hash
\ backslash or backwhack
/ slack or whack
forward slash or divide
* star or wildcard or asterisk
~ tilde or that wiggly line next to the one key
squiggle (next to RETURN, ENTER in UK)
_ underline, underscore
- dash, hyphen
. full stop, dot
` backtick, no not quote, the other one.

And that's only for single characters! What about compound character operators? 
Perl 6 can even take some unicode symbols as arithmetic operators!

On Mon, Mar 12, 2018 at 10:40 AM, Amy E. Hodge 
> wrote:

I found this very interesting. I also find that mixtures of cultural 
backgrounds in the class – or a difference between myself and the learners – 
can sometimes lead to confusion in the different ways people describe the 
symbols in particular.



I spent the first half day leading a week-long training (not for coding, but 
for something internal to the company I was working for where there was an 
internal “language” to be learned) before I realized that while I was 
describing them as “braces,” “square brackets,” and “parentheses,” my learners 
described these as “flower brackets,” “square brackets,” and “round brackets,” 
and the three together under the umbrella of “brackets,” which I only used in 
reference to the square ones. Learning got much faster after we got that 
squared away!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu

650.556.5194

[cid:image001.png@01D3B9DD.C20D7850] 
orcid.org/-0002-5902-3077



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: Discuss 
>
 on behalf of Lex Nederbragt 
>
Date: Monday, March 12, 2018 at 2:48 AM
To: Software Carpentry Discussion 
>
Subject: [Discuss] Code Phonology - on reading code aloud



Hi,



Felienne Hermans has a really interesting blog post and accompanying paper on 
Code Phonology, i.e. on reading code aloud: 
http://www.felienne.com/archives/5947.



This is relevant for teaching through ‘live follow-along coding’: are we aware 
what vocabulary we use and what effect that has on our learners (e.g. cognitive 
load)? Do we use consistent vocabulary across lessons and between workshops?



Food for thought...



Lex



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--
Kevin Vilbig

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The University of Dundee is a registered Scottish Charity, No: SC015096
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Re: [Discuss] resources on how to manage a virtual team

[David Martin (Staff)]

I'd suggest you arrange an in-person meeting. Preferably away from 
distractions. We had a great one for the ELM project at Barony Rosendal after 
the SOCBIN in Bergen about a decade ago. Ask Rein Aasland about that one.

You also have many good places on Voksenåsen and Holmenkollen for a suitable 
get together.

Once you have all met face to face it becomes a lot easier to work together 
remotely.


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss  on behalf of Karin 
Lagesen 
Sent: 26 February 2018 18:21
To: discuss@lists.software-carpentry.org
Subject: [Discuss] resources on how to manage a virtual team

I find myself in the position of being a work package leader for a EU
project. I don't know any of the ones that will work with me in this
work package, and they all work at different institutions all over
Europe. To boot, I have never managed a EU work package before.

Thus, I am looking for tips, links, books, whatever you might know of
that might help me forge these people into an actual team that gets
stuff done. I know there are a lot of researchers and others on this
list that might have been in the same situation as me, which is why I
thought asking via this list might garner some good results.

Thanks in advance,

Karin
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Re: [Discuss] Response to "Null effects of bootcamps ..." paper

[David Martin (Staff)]

A quick glance over the data indicates very small numbers. They are looking at 
~20-30 participants, not the nearly 300 total in the study.

There is also some doubt over the data collection - do the graduate students 
really write their research proposal completely independently? I would be most 
surprised if they did as a supervisor will want to get the best students 
admitted.


There is no power analysis to state what kind of effect they would expect to 
see in their scoring.


There are some valid points in the introduction. I don't see bootcamps as a way 
of teaching a competence, but teaching awareness of what that competence can 
bring. It still takes time and practice to develop the skills, which is a 
different thing than being aware that those skills can be developed.


..d


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss  on behalf of 
Belinda Weaver 
Sent: 11 December 2017 21:27
To: discuss@lists.software-carpentry.org
Subject: [Discuss] Response to "Null effects of bootcamps ..." paper

Hi everyone

A while back, a paper called “Null effects of boot camps and short-format 
training for PhD students in life 
sciences” appeared in 
the Proceedings of the National Academy of Sciences.

The paper sparked a lot of interest as it seemed to say that short workshops 
don't change anything.

The Carpentries wanted to challenge the idea that bootcamps don't work. 
Accordingly, Karen Word and others have written a response to that paper which 
is here:

http://www.datacarpentry.org/blog/reponse-to-null-effects/

Comments are welcome.

regards
Belinda


Belinda Weaver
Community Development Lead
Software and Data Carpentry
e: bwea...@carpentries.org | p: +61 408 841 882 
| t: @cloudaus

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Re: [Discuss] Your advice. Python lesson for really novice students

[David Martin (Staff)]

I would look at the domain they are interested in and have some simple code 
they can modify to make things happen – ie scripting how many circles, size, 
colour appear on screen. Simple buttons – maybe something like the gpiozero 
library and interaction with hardware would work well to demonstrate how code 
has real, physical effects.

I would expect for a taster lesson that it is about making the potential 
apparent, not actually learning any coding, but learning that through coding 
you can be empowered to make things happen. That then gives the motivation to 
learn the nuts and bolts.

..d

From: Discuss [mailto:discuss-boun...@lists.software-carpentry.org] On Behalf 
Of Javier García Algarra
Sent: 29 November 2017 14:45
To: Software Carpentry Discussion 
Subject: [Discuss] Your advice. Python lesson for really novice students

Hi all:
I am going to give an introductory lesson to students from 16 to 18 years old 
that do not
plan to follow a STEM path, but some digital-enabled artistic disciplines: 
animation, design and so on. This is an optional activity, so we assume that 
enrolled students have a strong motivation to learn programming basic skills. I 
plan to use the Pyhton lesson as a template, and I would
appreciate your advice to deal with this scenario.

Thanks in advance

Javier

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Re: [Discuss] SQL IFNULL question

[David Martin (Staff)]

Yes is the answer having actually installed the software and data with which to 
play (possibly procrastinating from grading papers).


SELECT surveys.plot_id, species.genus, count(species.genus) as observations
FROM surveys
JOIN species
ON IFNULL(surveys.species_id,'AB') = species.species_id
GROUP BY surveys.plot_id, species.genus;



Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of David 
Martin (Staff) <d.m.a.mar...@dundee.ac.uk>
Sent: 21 October 2017 00:01
To: Amy E. Hodge; discuss@lists.software-carpentry.org
Subject: Re: [Discuss] SQL IFNULL question


I think there is a philosophical difference between your solution with a left 
join and building on the example which does an inner join, but that may not be 
important in the long run. It is a case of how you are phrasing the question.


In your case you replicate the ifnull clause three times in the query wheras by 
including the ifnull in the join statement it is only present once and a single 
point of dependency (I think it is better on a DRY principle, others will have 
a different opinion)


Did my variant work? Did you determine the syntax error in your earlier 
attempts?


..d


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Amy E. Hodge <amyho...@stanford.edu>
Sent: 20 October 2017 23:42
To: David Martin (Staff); discuss@lists.software-carpentry.org
Subject: Re: SQL IFNULL question


Yes! This works:



SELECT surveys.plot_id, IFNULL(species.genus, 'Rodent'), 
COUNT(IFNULL(species.genus, 'Rodent'))

FROM surveys

LEFT JOIN species

USING (species_id)

GROUP BY surveys.plot_id, IFNULL(species.genus, 'Rodent');



Thanks!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194

[cid:image001.png@01D349BA.0A63BE50] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: "David Martin (Staff)" <d.m.a.mar...@dundee.ac.uk>
Date: Friday, October 20, 2017 at 3:08 PM
To: "Amy E. Hodge" <amyho...@stanford.edu>, 
"discuss@lists.software-carpentry.org" <discuss@lists.software-carpentry.org>
Subject: Re: SQL IFNULL question



SELECT surveys.plot_id, IFNULL(species.genus, 'Rodent'), 
COUNT(IFNULL(species.genus, 'Rodent'))

FROM surveys

LEFT JOIN species

USING (species_id)

GROUP BY surveys.plot_id, species.genus;

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096
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Re: [Discuss] SQL IFNULL question

[David Martin (Staff)]

I think there is a philosophical difference between your solution with a left 
join and building on the example which does an inner join, but that may not be 
important in the long run. It is a case of how you are phrasing the question.


In your case you replicate the ifnull clause three times in the query wheras by 
including the ifnull in the join statement it is only present once and a single 
point of dependency (I think it is better on a DRY principle, others will have 
a different opinion)


Did my variant work? Did you determine the syntax error in your earlier 
attempts?


..d


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Amy E. Hodge <amyho...@stanford.edu>
Sent: 20 October 2017 23:42
To: David Martin (Staff); discuss@lists.software-carpentry.org
Subject: Re: SQL IFNULL question


Yes! This works:



SELECT surveys.plot_id, IFNULL(species.genus, 'Rodent'), 
COUNT(IFNULL(species.genus, 'Rodent'))

FROM surveys

LEFT JOIN species

USING (species_id)

GROUP BY surveys.plot_id, IFNULL(species.genus, 'Rodent');



Thanks!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194

[cid:image001.png@01D349BA.0A63BE50] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: "David Martin (Staff)" <d.m.a.mar...@dundee.ac.uk>
Date: Friday, October 20, 2017 at 3:08 PM
To: "Amy E. Hodge" <amyho...@stanford.edu>, 
"discuss@lists.software-carpentry.org" <discuss@lists.software-carpentry.org>
Subject: Re: SQL IFNULL question



SELECT surveys.plot_id, IFNULL(species.genus, 'Rodent'), 
COUNT(IFNULL(species.genus, 'Rodent'))

FROM surveys

LEFT JOIN species

USING (species_id)

GROUP BY surveys.plot_id, species.genus;

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Re: [Discuss] SQL IFNULL question

[David Martin (Staff)]

OK, forgot the genus. You're grouping splits the data into the following groups:


Plot 1: genus 1, genus 2. Rodent, Null

then renames the null as Rodent, That is why you get two Rodent groups.  You 
have to ensure it joins properly, not leaving the hanging nulls or you need to 
include the ifnull in the group by


..d


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of David 
Martin (Staff) <d.m.a.mar...@dundee.ac.uk>
Sent: 20 October 2017 22:53
To: Amy E. Hodge; discuss@lists.software-carpentry.org
Subject: Re: [Discuss] SQL IFNULL question


SELECT surveys.year, surveys.month, surveys.day, species.genus, species.species
FROM surveys
JOIN species
ON IFNULL(surveys.species_id,'AB') = species.species_id;

is the example given which should work for joining and assigning species. You 
then have to change the select to give the count as you have done and include 
the group by


SELECT surveys.plot_id, count(distinct(species.genus))
FROM surveys
JOIN species
ON IFNULL(surveys.species_id,'AB') = species.species_id GROUP BY 
surveys.plot_id;


I've not downloaded the data to play with but that should be what you are 
looking for.


..d



Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Amy E. Hodge <amyho...@stanford.edu>
Sent: 20 October 2017 22:29
To: David Martin (Staff); discuss@lists.software-carpentry.org
Subject: Re: SQL IFNULL question


Yep, I looked at that W3schools page, but it didn’t help me out.



I hadn’t considered using the IFNULL in the join, but it doesn’t seem to like 
that. I’m getting a syntax error at “ON IFNULL”.



Also, your suggestion counts the number of distinct genera. My interpretation 
of this was that we were to count the number of each genera per plot, i.e. plot 
1 has 54  Baiomys, 28 Reithrodontomys, 4 Pipilo, etc.



This seems to work in general:



SELECT surveys.plot_id, IFNULL(species.genus, 'Rodent'), 
COUNT(IFNULL(species.genus, 'Rodent'))

FROM surveys

LEFT JOIN species

USING (species_id)

GROUP BY surveys.plot_id, species.genus;



But the cases where IFNULL converts NULL values to ‘Rodent’ aren’t being 
collapsed into the existing Rodent genus, so it’s confusingly listed twice in 
the search results for each plot where ‘Rodent’ was already on the list.



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194

[cid:image001.png@01D349AF.E0DD72B0] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: "David Martin (Staff)" <d.m.a.mar...@dundee.ac.uk>
Date: Friday, October 20, 2017 at 2:09 PM
To: "Amy E. Hodge" <amyho...@stanford.edu>, 
"discuss@lists.software-carpentry.org" <discuss@lists.software-carpentry.org>
Subject: Re: SQL IFNULL question



First time I have seen it. Try https://www.w3schools.com/sql/sql_isnull.asp



and wrap the species_id  in ifnull()  so



select count(distinct(s.genus))  from surveys as o  inner join species as s  on 
ifnull(o.species_id, 'RN') = s.species_id;



The tables are joined so every observation has a species, then you can reduce 
it to a single instance for each genus with distinct and count the number of 
rows with count( ) (iirc - it is a while since I have done this).

SQL ISNULL(), NVL(), IFNULL() and COALESCE() 
Functions<https://www.w3schools.com/sql/sql_isnull.asp>

www.w3schools.com

Well organized and easy to understand Web building tutorials with lots of 
examples of how to use HTML, CSS, JavaScript, SQL, PHP, and XML.






Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee





From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of Amy 
E. Hodge <amyho...@stanford.edu>
Sent: 20 October 2017 21:59
To: discuss@lists.software-carpentry.org
Subject: [Discuss] SQL IFNULL question



Hi all,



I’ll be teaching from 
http://www.datacarpentry.org/sql-ecology-lesson/03-sql-joins-aliases/ soon, and 
realized there is a section here on IFNULL and NULLIF that I haven’t taught 
before. In all my years of using SQL, I’ve never even heard of these functions! 
So, I’m trying to learn this quickly.

SQL for Ecology: Joins and aliases - Data 
Carpentry<http://www.datacarpentry.org/sql-ecology-lesson/03-sql-joins-aliases/>

www.datacarpentry.org

Employ joins to combine data from two tables. Apply functions to manipulate 
individual values. Employ aliases to assign new names to items in a query. To 
combine data ...






I cannot seem to wrap my brain around how to do 

Re: [Discuss] SQL IFNULL question

[David Martin (Staff)]

SELECT surveys.year, surveys.month, surveys.day, species.genus, species.species
FROM surveys
JOIN species
ON IFNULL(surveys.species_id,'AB') = species.species_id;

is the example given which should work for joining and assigning species. You 
then have to change the select to give the count as you have done and include 
the group by


SELECT surveys.plot_id, count(distinct(species.genus))
FROM surveys
JOIN species
ON IFNULL(surveys.species_id,'AB') = species.species_id GROUP BY 
surveys.plot_id;


I've not downloaded the data to play with but that should be what you are 
looking for.


..d



Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Amy E. Hodge <amyho...@stanford.edu>
Sent: 20 October 2017 22:29
To: David Martin (Staff); discuss@lists.software-carpentry.org
Subject: Re: SQL IFNULL question


Yep, I looked at that W3schools page, but it didn’t help me out.



I hadn’t considered using the IFNULL in the join, but it doesn’t seem to like 
that. I’m getting a syntax error at “ON IFNULL”.



Also, your suggestion counts the number of distinct genera. My interpretation 
of this was that we were to count the number of each genera per plot, i.e. plot 
1 has 54  Baiomys, 28 Reithrodontomys, 4 Pipilo, etc.



This seems to work in general:



SELECT surveys.plot_id, IFNULL(species.genus, 'Rodent'), 
COUNT(IFNULL(species.genus, 'Rodent'))

FROM surveys

LEFT JOIN species

USING (species_id)

GROUP BY surveys.plot_id, species.genus;



But the cases where IFNULL converts NULL values to ‘Rodent’ aren’t being 
collapsed into the existing Rodent genus, so it’s confusingly listed twice in 
the search results for each plot where ‘Rodent’ was already on the list.



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194

[cid:image001.png@01D349AF.E0DD72B0] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305



From: "David Martin (Staff)" <d.m.a.mar...@dundee.ac.uk>
Date: Friday, October 20, 2017 at 2:09 PM
To: "Amy E. Hodge" <amyho...@stanford.edu>, 
"discuss@lists.software-carpentry.org" <discuss@lists.software-carpentry.org>
Subject: Re: SQL IFNULL question



First time I have seen it. Try https://www.w3schools.com/sql/sql_isnull.asp



and wrap the species_id  in ifnull()  so



select count(distinct(s.genus))  from surveys as o  inner join species as s  on 
ifnull(o.species_id, 'RN') = s.species_id;



The tables are joined so every observation has a species, then you can reduce 
it to a single instance for each genus with distinct and count the number of 
rows with count( ) (iirc - it is a while since I have done this).

SQL ISNULL(), NVL(), IFNULL() and COALESCE() 
Functions<https://www.w3schools.com/sql/sql_isnull.asp>

www.w3schools.com

Well organized and easy to understand Web building tutorials with lots of 
examples of how to use HTML, CSS, JavaScript, SQL, PHP, and XML.






Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee





From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of Amy 
E. Hodge <amyho...@stanford.edu>
Sent: 20 October 2017 21:59
To: discuss@lists.software-carpentry.org
Subject: [Discuss] SQL IFNULL question



Hi all,



I’ll be teaching from 
http://www.datacarpentry.org/sql-ecology-lesson/03-sql-joins-aliases/ soon, and 
realized there is a section here on IFNULL and NULLIF that I haven’t taught 
before. In all my years of using SQL, I’ve never even heard of these functions! 
So, I’m trying to learn this quickly.

SQL for Ecology: Joins and aliases - Data 
Carpentry<http://www.datacarpentry.org/sql-ecology-lesson/03-sql-joins-aliases/>

www.datacarpentry.org

Employ joins to combine data from two tables. Apply functions to manipulate 
individual values. Employ aliases to assign new names to items in a query. To 
combine data ...






I cannot seem to wrap my brain around how to do this Challenge, and there is no 
answer key. (Also, plural of “genus” is “genera”!)



· Write a query that returns the number of genus of the animals caught 
in each plot, using IFNULL to assume that unknown species are all of the genus 
“Rodent”.



I’m at a loss as to how to replace NULL values in genus field with a value 
based on what is in the species_id field.



Can someone help me out? Thanks!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu<mailto:amyho...@stanford.edu>

650.556.5194

[cid:image002.png@01D349AF.E0DD72B0] 
orcid.org/-0002-5902-3077<https://orcid.org/-0002-5902-3077>



Data Management Services
Branner Earth Sciences Library, 

Re: [Discuss] SQL IFNULL question

[David Martin (Staff)]

First time I have seen it. Try https://www.w3schools.com/sql/sql_isnull.asp


and wrap the species_id  in ifnull()  so


select count(distinct(s.genus))  from surveys as o  inner join species as s  on 
ifnull(o.species_id, 'RN') = s.species_id;


The tables are joined so every observation has a species, then you can reduce 
it to a single instance for each genus with distinct and count the number of 
rows with count( ) (iirc - it is a while since I have done this).

SQL ISNULL(), NVL(), IFNULL() and COALESCE() 
Functions
www.w3schools.com
Well organized and easy to understand Web building tutorials with lots of 
examples of how to use HTML, CSS, JavaScript, SQL, PHP, and XML.




Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss  on behalf of Amy 
E. Hodge 
Sent: 20 October 2017 21:59
To: discuss@lists.software-carpentry.org
Subject: [Discuss] SQL IFNULL question


Hi all,



I’ll be teaching from 
http://www.datacarpentry.org/sql-ecology-lesson/03-sql-joins-aliases/ soon, and 
realized there is a section here on IFNULL and NULLIF that I haven’t taught 
before. In all my years of using SQL, I’ve never even heard of these functions! 
So, I’m trying to learn this quickly.

SQL for Ecology: Joins and aliases - Data 
Carpentry
www.datacarpentry.org
Employ joins to combine data from two tables. Apply functions to manipulate 
individual values. Employ aliases to assign new names to items in a query. To 
combine data ...





I cannot seem to wrap my brain around how to do this Challenge, and there is no 
answer key. (Also, plural of “genus” is “genera”!)



  *   Write a query that returns the number of genus of the animals caught in 
each plot, using IFNULL to assume that unknown species are all of the genus 
“Rodent”.



I’m at a loss as to how to replace NULL values in genus field with a value 
based on what is in the species_id field.



Can someone help me out? Thanks!



~ Amy



Amy E. Hodge, PhD
Science Data Librarian

amyho...@stanford.edu

650.556.5194

[cid:image001.png@01D349AB.AD6FD8E0] 
orcid.org/-0002-5902-3077



Data Management Services
Branner Earth Sciences Library, 212 Mitchell
397 Panama Mall; MC 2211
Stanford University
Stanford, CA 94305

The University of Dundee is a registered Scottish Charity, No: SC015096
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Re: [Discuss] Know of anything like "Nature, In Code"

[David Martin (Staff)]

Does Python for Biologists meet your requirements? Teaches Python from a 
molecular biology problems perspective.


..d


Dr David Martin
Senior Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss  on behalf of Pat 
Schloss 
Sent: 20 September 2017 19:29
To: Software Carpentry Discussion
Subject: [Discuss] Know of anything like "Nature, In Code"

Hi everyone,

I was wondering whether anyone knows of other books/MOOCs/resources that are 
similar to “Nature, In Code”. I’m looking for something that teaches biology 
via programming or perhaps teaches programming via biology - to me this is 
pretty different than a typical programming or even bioinformatics book. 
“Nature, In Code” is written to help people learn Javascript.

Thanks,
Pat


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Re: [Discuss] Teaching Git with Github Desktop

[David Martin (Staff)]

> Git command line interface isn't friendly to new users because "git checkout" 
> do too much for the same command depending of what arguments the user pass.

> Why do we can't have "git undo" that ony works with the working copy?

alias 'git undo' 'git checkout ...'

> Why do we can't have "git recovery" that only works with old revisions?

alias 'git recover' 'git checkout ...'

> As a intermediate user I understand why all the actions previous mentioned 
> are under "git checkout" but for a new user this isn't clear.

Or you could suggest it as a feature to extend the command set..

Each has their place. Command line causes users to slow down and think. GUI 
tools (like sourcetree or Kraken) make it much easier in a heterogeneous 
environment.

We teach basic principles before kits, and command line before GUI because we 
teach the why rather than just the what.

..d


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[Discuss] FW: [nextgenbug] First conference for Research Software Engineers

[David Martin (Staff)]

This may well be of interest to folk – maybe there should be a ‘growing the 
next research software engineers’ offering?

..d

From: nextgenbug-arch...@googlegroups.com 
[mailto:nextgenbug-arch...@googlegroups.com] On Behalf Of Sujai Kumar
Sent: 10 May 2016 09:40
To: ashworth-code-monk...@googlegroups.com; nextgenbug-arch...@googlegroups.com
Subject: [nextgenbug] First conference for Research Software Engineers

(forwarding on behalf of Simon Hettrick 
s.hettr...@software.ac.uk)

RSE Conference - Call for Participation---
===

The RSE Conference is the first conference to focus exclusively on the issues 
that affect people who write and use software in research. We're looking for 
submissions to our workshops and talks programmes that will investigate and 
communicate ideas and expertise from the RSE community.

It is not a standard academic conference! We welcome researchers, but we also 
want to hear from people who may not typically attend conferences. It’s a 
community conference: get involved and help us build the RSE Community.

From running a workshop, sharing your ideas or simply attending, there are many 
ways in which you can participate. We want to hear from you about the new 
technologies and techniques that help you in your work. We want your opinions 
on what will make the conference even more useful. And, of course, we want you 
to attend!

We’ve described the many different ways you can participate below. Take a look, 
and get in touch if you’d like more information.

---Call for workshops---

If you want to help others learn about a new tool, technology or methodology, 
then please submit a workshop.

More information: http://www.rse.ac.uk/conf2016_calls_workshops

---Call for talks---

We’re looking for talks that discuss and expand on issues that affect RSEs.

More information: http://www.rse.ac.uk/conf2016_calls_talks

---What’s an RSE?---

Research Software Engineers are the people who work in research, but write code 
not papers. Most people who conduct the work of an RSE are not formally called 
a Research Software Engineer.

More information: http://www.rse.ac.uk/who.

---Who should take part?---

We’re looking for participation from anyone with an interest in software in 
research: people who develop software (regardless of your job title), 
researchers, people who provide tools. It doesn’t matter if you’ve never 
attended a conference before, if you have an interest in software, we want to 
hear from you!

We’re actively encouraging first-time speakers and workshop leaders to take 
part, and we’re offering support and mentoring to those people who would like 
it.

---Tell us what to do!---

To make the conference a success, we want to hear from the community about what 
they would like to see at the conference. Got a good idea (or even a criticism)?

Please get in touch: i...@rse.ac.uk.

---UKRSE AGM---

We will also be holding the UKRSE Annual General Meeting during the conference. 
This is your chance to influence the community through discussions, voting or 
by standing for an official role.

---Attend!---

Attendees will learn about the cutting edge techniques being used in research, 
pick up new skills, and hear from a broad range of speakers.

Registration will open in June and will cost £75. We’re limited to 150 
attendees at this first conference. If you provide your contact details, we’ll 
send you a reminder once registration is 
open:http://www.rse.ac.uk/conf2016_registration

---Other participation---

There are many ways to support this first community conference for RSEs, from 
volunteering to sponsorship.

More information: http://www.rse.ac.uk/conf2016

---Contact---

Email the organisers at i...@rse.ac.uk

Tweet about the conference: @ResearchSoftEng #RSE16
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For more options, 

Re: [Discuss] Word and PowerPoint "all wrong"?

[David Martin (Staff)]

Training wheels on a bike are actually all wrong. They encourage bad practice 
and do not develop the correct approach, making transition harder.

For those who are interested: To teach someone to ride a bike, first teach them 
to scoot and balance. Typically that involves putting the seat to a level where 
they can comfortably reach the floor, and taking the pedals off. Scoot and 
balance. Once that is picked up, add the pedals back in.

Training wheels seem like a nice idea but are actually counterproductive.

Now apply that to your software/scientific computing paradigm of choice. (Using 
the undo button as version control?)

..d

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss  on behalf of 
Michael J Jackson 
Sent: 05 May 2016 10:02:05
To: Timothy Rice
Cc: discuss@lists.software-carpentry.org; Dirk Eddelbuettel
Subject: Re: [Discuss] Word and PowerPoint "all wrong"?

Hi Timothy,

Quoting Timothy Rice  on Thu, 5 May 2016
07:28:51 +1000:

> Are training wheels on a bike "all wrong"?
>
> To a beginner, training wheels also seem to have points of superiority; yet
> we expect that as time goes on, the novice will discard the training
> wheels. This is both a display of increased skill, and a prerequisite for
> using the bike more effectively overall.
>
> But maybe when even all the adults use training wheels too, and they can't
> imagine a bike without training wheels, this state of affairs would hold
> people back from using the bike to its full potential. It might even turn
> out that anyone who does take the initiative of discarding training wheels
> would seem like a freak who has to justify themselves to others. They might
> find themselves responding to claims that training wheels aren't "all
> wrong" ;)
>
> And, you know, one of the things I emphasise at the start when teaching
> LaTeX is that it is contraindicated for small, uncomplicated projects that
> don't have special typesetting requirements. If someone is just writing a
> letter to their grandma, they might wish to stick with their conventional
> word processor, it's no skin off my nose.
>
> However, one would hope that in academia, the researcher aspires to create
> non-trivial documents; certainly many people who have tried writing a
> thesis in Word later came to lament their choice.

Yes, I'm one of them!

> Are Word and PowerPoint "all wrong"? Maybe not. But should we be content
> with software whose main claim to fame is that they're not all wrong and
> they happen to be used by a lot of people who refuse to discard training
> wheels?

The "training wheels" analogy does not hold. Word and PowerPoint are
not designed for beginners only. They are powerful document
preparation tools in their own right.

My point was that Word and PowerPoint are not "all wrong" nor are they
"all right". They have strengths and weaknesses, as does LaTeX (great
for formulae!). Statements that can be perceived as fundamentalist
("all wrong") or patronising ("training wheels") when promoting one
tool over another does no favours and can be counter-productive. As an
example, I've seen attendees at a workshop ask if they can hold Word
docs under Git and, when told, "ideally you'd use plain-text documents
to get the most benefit", switch off entirely as their community used
Word, but when told "of course, you can put Word docs under Git", and
having been shown this (including how to do a simple conflict
resolution), brighten up again. I'd rather people be taught to
appreciate and be aware of the strengths and weaknesses of all the
tools they use, and, as Jan mentions, the technical debts they could
incur. This includes the tools currently used by SWC (which, in
future, people may wonder why we ever used some of them - a colleague
recently railed against using a closed source platform like GitHub,
for example)

cheers,
mike

> Kind regards,
>
>
> Tim
>
> [1] https://github.com/cryptarch/latex-novice.git




>
>> As one who writes everything in MarkDown by preference, are Word and
>> PowerPoint "all wrong"? Yes, their binary formats don't play so well
>> with revision control than plain-text formats such as MarkDown or
>> LaTeX, for example (but sticking them under revision control is
>> still of great benefit). In other ways they're superior: WYSIWYG
>> editors, no compilation steps, PDF-generation from within the tool,
>> and they're ubiquitous. Similarly, for some tasks they allow a user
>> to "do more in less time with less pain" than the alternatives*.
>>
>> cheers,
>> mike
>>
>> * Having spent more than the 5 minutes it should have taken
>> yesterday trying (and failing even with Google's help) to put a
>> hyperlink to a Wikipedia page with multiple underscores in a LaTeX
>> document and have it clickable in the resulting PDF.

Re: [Discuss] "Stealing Google's coding practices for academia"

[David Martin (Staff)]

So in my undergraduate teaching we already use Git (which after a little pain 
they get to really enjoy - the easiest way is to make them work on 
collaborative projects) but after reading that I will be encouraging the use of 
the style guide and pylint (just working out how to use it myself).

A formal onboarding process (that we can agree on across groups and roll into 
teaching) is probably a very good thing. Avoiding Hobgoblins of course.

..d

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss  on behalf of 
Marianne Corvellec 
Sent: 02 May 2016 21:00
To: Neil Chue Hong (SSI)
Cc: Software Carpentry Discussion
Subject: Re: [Discuss] "Stealing Google's coding practices for academia"

Thanks, Titus!

That was a long but amazing read.

My personal favourites:
"""
- Fix bugs, everyone gets epsilon happier.

- What?  You're an academic research group that doesn't have a formal
onboarding process?

- I have a hypothesis that better testing might make it substantially
easier to have summer interns or short-term undergrads work in your
group.
"""

On Mon, May 2, 2016 at 5:19 AM, Neil Chue Hong (SSI)
 wrote:
> Thanks for passing it on - that's one of the best "how to actually use
> this stuff without it getting in the way of what you're trying to do"
> posts I've seen in a while.
>
> Neil
>
> On 30 April 2016 at 14:18, C. Titus Brown  wrote:
>> Have people seen this? I didn’t see it make the rounds, but it’s one of the 
>> nicest meso-depth writeups on what to do in your lab I’ve seen --
>>
>> http://da-data.blogspot.com/2016/04/stealing-googles-coding-practices-for.html
>>
>> cheers,
>> —titus
>>
>>
>> ___
>> Discuss mailing list
>> Discuss@lists.software-carpentry.org
>> http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org
>
>
>
> --
> Neil Chue Hong
> Director, Software Sustainability Institute
> EPCC, University of Edinburgh, JCMB, Edinburgh, EH9 3FD, UK
> Tel: +44 (0)131 650 5957
> http://www.software.ac.uk/
>
> LinkedIn: http://uk.linkedin.com/in/neilchuehong
> Twitter: http://twitter.com/npch
> ORCID: http://orcid.org/-0002-8876-7606
>
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Re: [Discuss] RajLab: From reproducibility to over-reproducibility

[David Martin (Staff)]

> We need to do better at emphasizing that these are skills that need to be 
> developed early and often, and not when you're in the middle of trying to 
> complete a project.

The "Why do I need to learn to swim? I'll wait till I am actually drowning 
otherwise it is a waste of time" approach.

..d
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Re: [Discuss] RajLab: From reproducibility to over-reproducibility

[David Martin (Staff)]

We spend about 50 contact hours teaching our undergraduates the basics of R. 
Even that is not enough. It has been said that you need 100 hours to reach 
competency, and 1000 hours to master a subject. And the next stage is 10,000 
hours to be an expert..

How much time has he invested in actually learning those skills? I was totting 
up the time we spend teaching X versus the amount of complaints we get that the 
students don't know X. There is a strong inverse correlation. Folk want a cheap 
easy fix and have been promised that with computers. It does exist but it has 
to be earned. You don't get cheap and easy for free.

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss  on behalf of Lex 
Nederbragt 
Sent: 29 February 2016 20:43
To: Software Carpentry Discussion
Subject: Re: [Discuss] RajLab: From reproducibility to over-reproducibility

Hi all and thanks for the many responses.

My feeling reading this post was about tools (partly echoing Greg): 'we' know 
'all of us' should use the appropriate tool, e.g. version control (is that what 
you call the moral high-ground?). But for the novice, these tools/methods have 
steep learning curves, thus high upfront time investment, and no immediate 
benefit (!!!). There is a burden on 'us' to convince 'others' of the need to 
invest time to adopt these tools.

I am not sure whether more convincing (how? Research-based evidence?) or 
training is the answer, versus much easier to learn and use tools.

   Lex
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Re: [Discuss] RajLab: From reproducibility to over-reproducibility

[David Martin (Staff)]

One reason why I like to use graphical clients such as SourceTree for Git. It 
hides much of the pain. Part of it is training and experience. It takes some 
time to be familiar with appropriate record keeping in a lab book. The same is 
true of using any software. I don't know why there is such an entitlement 
culture of it being easy, or not something that has to be practiced till it is 
got right.

..d

From: Discuss [mailto:discuss-boun...@lists.software-carpentry.org] On Behalf 
Of Greg Wilson
Sent: 29 February 2016 16:25
To: Software Carpentry Discussion 
Subject: Re: [Discuss] RajLab: From reproducibility to over-reproducibility

The biggest thing I'm taking away from this blog post is that lousy interfaces 
and obscure failure modes really are inhibiting adoption of better computing 
practices.  From the post:


if you're like me, you will screw up at some point, leading to some problem, 
potentially catastrophic, that you will spend hours trying to figure out. I'm 
clearly not alone... "Abort: remote heads forked" anyone? :) At that point, we 
all just call over the one person in lab who knows how to deal with all this 
crap and hope for the best. And look, I'm relatively computer savvy, so I can 
only imagine how intimidating all this is for people who are less computer 
savvy.

I heard fewer complaints of this kind, and believe that I saw higher adoption 
rates, when we were teaching Subversion.  I'm not going to recommend that we 
switch back, but I do miss it whenever I have to help someone deal with a 
detached head...

Thanks,
Greg



--

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Director of Instructor Training

Software Carpentry Foundation

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Re: [Discuss] Reproducible computing -- some thoughts and questions

[David Martin (Staff)]

What you are doing is pointing out that research that is not robust is as 
poorly reproducible as research that is insufficiently documented.

If I have to worry about specific compiler versions giving vastly different 
results in my analysis then it is not the fault of the system so much as my 
choice of analysis methods being somewhat less than robust. (Yes there are 
cases where there are specific packages that are wrong - I mean the different 
cases of 'right').

So teaching reproducible research is also about teaching robust research, that 
is not dependent on the exact microenvironment but can be replicated anywhere 
similar.

..d

-Original Message-
From: Discuss [mailto:discuss-boun...@lists.software-carpentry.org] On Behalf 
Of David Jones
Sent: 14 January 2016 15:46
To: Titus Brown 
Cc: Software Carpentry Discussion 
Subject: Re: [Discuss] Reproducible computing -- some thoughts and questions

On 14 January 2016 at 15:18, C. Titus Brown  wrote:
>
> (Agree with most of this; I'm just hesitant to say anything nice about
> ugly heavy binary images :)

I think everyone is a little bit hesitant to say anything nice about ugly heavy 
binary images.

And I think part of that stems from the fact that the things we do really do 
depend on a whole load of ugly heavy things. And the way to capture that is to 
capture a whole load of ugly heavy binary things.
We're reluctant to face the reality.

When we try and optimise that (by say, a Dockerfile, or a list of conda package 
versions) we're building a model, and we're saying, at least implicitly, I 
don't care about various minor uninteresting things (for example that security 
updates change the exact set of files that are "ubuntu:14.04").

Of course, a binary VM image or the nested tar files of a Docker image are only 
a model too. I can easily write a script whose output depends on the CPU ID of 
the CPU in my laptop. Clearly that's never going to be reproducible.

I think it's useful to bear in mind that to some extent reproducibility is a 
modelling exercise.

"All models are wrong but some are useful" - George Box

drj

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Re: [Discuss] conferences featuring basic computer science education?

[David Martin (Staff)]

This one just popped into my mailbox. http://eams.ncl.ac.uk/ - more focussed on 
e-assessment in mathematical sciences.


Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss  on behalf of Susan 
McClatchy 
Sent: 14 January 2016 18:45
To: discuss@lists.software-carpentry.org
Subject: [Discuss] conferences featuring basic computer science education?

Hi,

Can any of you recommend conferences with strong basic computer science 
education components? The best focus would be undergraduate and higher 
computing education in the sciences.

Thanks,

Sue


Sue McClatchy, M.S.
Bioinformatician & Research Program Manager | The  Center 
for Genome Dynamics | The Jackson 
Laboratory
207.288.6431
susan.mcclat...@jax.org


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Re: [Discuss] changes merged to shell-novice lesson

[David Martin (Staff)]

Could I make a request on substantive changes to lessons.


This change has been 'interesting' when we are in the middle of a SWC workshop. 
Having downloaded and tested the previous version, got to the workshop to 
discover that half the material was missing. This led to some scrambling.


So please - if a lesson is being substantially rewritten (rather than just 
cosmetic/minor changes) then place it under a different name for a period of 
time (at least a fortnight, preferably a month) until it can be accepted as the 
new definitive version with time for scheduled workshops to adapt/adopt it.

It is most unfair/unprofessional to expect instructors to be responding on the 
hoof to changes underfoot.



Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss  on behalf of Greg 
Wilson 
Sent: 10 January 2016 02:28
To: Christina Koch; Software
Subject: Re: [Discuss] changes merged to shell-novice lesson

Thanks very much for your work on this, Christina - really appreciate it.
- Greg

On 2016-01-09 3:54 PM, Christina Koch wrote:
Hi everyone,

Heads-up to those of you teaching in the next few weeks - my fairly significant 
rewrite of the files-directories piece of the shell-novice lesson has finally 
been merged, so things will look different going forward.  We probably didn't 
catch *all* the bugs in PR review, so please let us know when you encounter 
problems - either file an issue or issue a PR and I'll try to prioritize and 
merge those.

I'll also have Maneesha email upcoming instructors just to make sure everyone 
hears about the change.

Cheers,
Christina

--
Christina Koch - Research Computing Facilitator,
University of Wisconsin - Madison, Center for High Throughput Computing
Advanced Computing Initiative; Wisconsin Institute for Discovery; ACI-REF
cko...@wisc.edu // (608) 316 - 4041 // 
tinyurl.com/ChristinaCalendarCHTC



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Re: [Discuss] changes merged to shell-novice lesson

[David Martin (Staff)]

I did. It doesn't work with github.io as changes to the .md are not propagated 
to the html.

There is something leftover from previous page generation methods that is not 
working with github.io.



Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Vilbig, Kevin P <kevin.vil...@mavs.uta.edu>
Sent: 11 January 2016 16:46
To: David Martin (Staff); Greg Wilson; Christina Koch; Software
Subject: Re: [Discuss] changes merged to shell-novice lesson


http://fu9ar.github.io/shell-novice/


Fork the repo and use the github.io page.


From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of David 
Martin (Staff) <d.m.a.mar...@dundee.ac.uk>
Sent: Monday, January 11, 2016 10:21 AM
To: Greg Wilson; Christina Koch; Software
Subject: Re: [Discuss] changes merged to shell-novice lesson


Could I make a request on substantive changes to lessons.


This change has been 'interesting' when we are in the middle of a SWC workshop. 
Having downloaded and tested the previous version, got to the workshop to 
discover that half the material was missing. This led to some scrambling.


So please - if a lesson is being substantially rewritten (rather than just 
cosmetic/minor changes) then place it under a different name for a period of 
time (at least a fortnight, preferably a month) until it can be accepted as the 
new definitive version with time for scheduled workshops to adapt/adopt it.

It is most unfair/unprofessional to expect instructors to be responding on the 
hoof to changes underfoot.



Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee




From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of Greg 
Wilson <gvwil...@software-carpentry.org>
Sent: 10 January 2016 02:28
To: Christina Koch; Software
Subject: Re: [Discuss] changes merged to shell-novice lesson

Thanks very much for your work on this, Christina - really appreciate it.
- Greg

On 2016-01-09 3:54 PM, Christina Koch wrote:
Hi everyone,

Heads-up to those of you teaching in the next few weeks - my fairly significant 
rewrite of the files-directories piece of the shell-novice lesson has finally 
been merged, so things will look different going forward.  We probably didn't 
catch *all* the bugs in PR review, so please let us know when you encounter 
problems - either file an issue or issue a PR and I'll try to prioritize and 
merge those.

I'll also have Maneesha email upcoming instructors just to make sure everyone 
hears about the change.

Cheers,
Christina

--
Christina Koch - Research Computing Facilitator,
University of Wisconsin - Madison, Center for High Throughput Computing
Advanced Computing Initiative; Wisconsin Institute for Discovery; ACI-REF
cko...@wisc.edu<mailto:cko...@wisc.edu> // (608) 316 - 4041 // 
tinyurl.com/ChristinaCalendarCHTC<http://tinyurl.com/ChristinaCalendarCHTC>



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gvwil...@software-carpentry.org<mailto:gvwil...@software-carpentry.org>
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Re: [Discuss] a new look for the Software Carpentry website

[David Martin (Staff)]

I've tried cloning a lesson to adapt for our local setup but none of the 
changes in the Markdown seem to be being propagated to the github-pages.
I've tried:
removing the .nojekyll
running jekyll from the command line (on a windows install because that's what 
I have available).

None of the changes arepropagated to the HTML.
What am I missing here?
..d

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss  on behalf of Greg 
Wilson 
Sent: 30 December 2015 08:40
To: Software Carpentry Discussion
Subject: [Discuss] a new look for the Software Carpentry website

Hi everyone,

The Software Carpentry website has a new look, and is in a new
repository - please make contributions to
https://github.com/swcarpentry/website (instead of the old
https://github.com/swcarpentry/site) from now on.  We think the new site
will be a lot easier to contribute to - instructions are in README.md -
and yes, you can now write blog posts for us in Markdown :-)
Contributions of all kinds are very welcome.

Happy Hogmanay,
Greg

p.s. we'll be rolling out updates to the workshop template and lesson
template over the next few days to give them the same appearance as the
updated web site.  These will *not* affect existing workshop websites,
and shouldn't require any changes to lesson content.

--
Dr. Greg Wilson| gvwil...@software-carpentry.org
Software Carpentry | http://software-carpentry.org


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Re: [Discuss] a new look for the Software Carpentry website

[David Martin (Staff)]

OK, following on from this. I create a new page by copying one of the existing 
pages. Delete all but the front matter and then add content. All I get in the 
generated HTML is placeholders. The actual data is missing.
ie. the generated HTML has
Software Carpentry: $pagetitle$
What is the magic 'extra'  that is undocumented and doesn't work out of the box 
that I am missing?




Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of David 
Martin (Staff) <d.m.a.mar...@dundee.ac.uk>
Sent: 09 January 2016 12:25
To: Greg Wilson; Software Carpentry Discussion
Subject: Re: [Discuss] a new look for the Software Carpentry website

I've tried cloning a lesson to adapt for our local setup but none of the 
changes in the Markdown seem to be being propagated to the github-pages.
I've tried:
removing the .nojekyll
running jekyll from the command line (on a windows install because that's what 
I have available).

None of the changes arepropagated to the HTML.
What am I missing here?
..d

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of Greg 
Wilson <gvwil...@software-carpentry.org>
Sent: 30 December 2015 08:40
To: Software Carpentry Discussion
Subject: [Discuss] a new look for the Software Carpentry website

Hi everyone,

The Software Carpentry website has a new look, and is in a new
repository - please make contributions to
https://github.com/swcarpentry/website (instead of the old
https://github.com/swcarpentry/site) from now on.  We think the new site
will be a lot easier to contribute to - instructions are in README.md -
and yes, you can now write blog posts for us in Markdown :-)
Contributions of all kinds are very welcome.

Happy Hogmanay,
Greg

p.s. we'll be rolling out updates to the workshop template and lesson
template over the next few days to give them the same appearance as the
updated web site.  These will *not* affect existing workshop websites,
and shouldn't require any changes to lesson content.

--
Dr. Greg Wilson| gvwil...@software-carpentry.org
Software Carpentry | http://software-carpentry.org


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Re: [Discuss] pulling along those behind

[David Martin (Staff)]

What Karin says.

Even in a less pressured environment there is no hope of someone turning up to 
a SC workshop and coming out of it a fully functioning and competent person int 
he areas they have been exposed to. However, what we have done, as instructors, 
is to sketch the route map and show how the concepts link together. The best 
students will spend 3x longer than the contact hours going back over it and 
learning the material thoroughly as they apply it.

..d

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Discuss  on behalf of Karin 
Lagesen 
Sent: 28 October 2015 20:11
To: discuss@lists.software-carpentry.org
Subject: Re: [Discuss] pulling along those behind

One of the things that I always emphasize before and during the workshop
is that my aim is not to teach them to be programmers, but to make it
less scary if and when they do decide to learn things more in depth. My
main goal is to demystify programming. That way, it becomes less about
understanding every detail and more about finding out that it is not as
complicated as it looks. I think that by doing that, even if I do lose
somebody on the little things, I manage to keep them with me on the
bigger, more conceptual things, if that makes sense.

Karin


On 27/10/15 17:38, Bill Mills wrote:
> I stretch the skill-level bracket of all my workshops by leaning heavily
> on tiered challenge problems; I break for problems regularly (every 30
> minutes or so, giving those really struggling a chance to catch up), and
> set 'baseline' problems (that everyone is expected to solve) and
> 'stretch' goals - harder problems that the intermediates can derive
> value from.
>
> On Tue, Oct 27, 2015 at 9:33 AM, Noam Ross  > wrote:
>
> One thing that I've found is that students who are behind sometimes
> give up trying to type along and just read along with the lesson
> notes.  While it's not the ideal outcome, it may be the best one for
> some fraction of students, and this makes it easier for those
> students to reference those notes at some later time.  So it might
> be worthwhile to point students to each lesson's notes before
> starting that section.
>
> On Tue, Oct 27, 2015 at 12:29 PM C. Titus Brown  > wrote:
>
> Hi Amanda et al.,
>
> thanks, this is a nice discussion!
>
> I try to distinguish between "zero entry" and more advanced
> workshops
> as clearly as possible, but of course problems happen in both
> directions
> for the advanced workshops - too advanced, and too beginner.
>
> One strategy that (I think) Greg suggested a long time ago was
> to suggest
> that the too-advanced people help out with the too-beginner
> people when
> a TA wasn't available.  Of course this can go wrong as well, but
> I think
> when it goes well it's quite nice.
>
> cheers,
> --titus
>
> On Tue, Oct 27, 2015 at 03:46:12PM +, Amanda Charbonneau wrote:
>  > I actually had a similar problem, but with an intro workshop
> that I had
>  > already pared down considerably because I knew the learners
> were skewed
>  > towards *very* beginners. Even with the simplified material,
> I had a
>  > handful of people who couldn't keep up, people who had to
> hover a single
>  > finger back and forth over the keyboard to locate each letter.
>  > This handful of people comprised about a quarter of the
> attendees, and
>  > the advertising clearly said that the course was for learners
> who have
>  > little to no prior computational experience, so they hadn't
> really gone to
>  > the wrong course level. It was just that their interpretation
> of no prior
>  > computational experience was very different from what SWC
> expects. It felt
>  > wrong to just press on without them, so I slowed everything
> down to a
>  > crawl, but I also felt extremely bad that we only got partway
> through any
>  > of the material.
>  >
>  > Sorry I don't have a solution, just commiseration.
>  >
>  > -amanda
>  >
>  > On Tue, Oct 27, 2015 at 11:24 AM Peter Steinbach
> >
>  > wrote:
>  >
>  > > Hi April,
>  > >
>  > > thanks for your insights. As a matter of fact, in my case
> the local
>  > > organizers were very forthcoming and implemented a
> pre-assessment form
>  > > before the workshop. Still, I had the 

Re: [Discuss] pulling along those behind

[David Martin (Staff)]

I encourage the students to break it in a known way so they can recognise the 
error messages. 'What happens if you forget to close the quote/miss out the 
comma' etc. Now you know what error you get so you know what to look for if you 
see that error again (unclosed quote/missing comma etc.)

If you are not failing some of the time then you are not trying hard enough 
problems. If you are not succeeding some of the time then the problems are too 
hard.

..d

Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee



From: Karin Lagesen <karin.lage...@gmail.com>
Sent: 28 October 2015 20:54
To: Sam Penrose; David Martin (Staff)
Cc: discuss@lists.software-carpentry.org
Subject: Re: [Discuss] pulling along those behind

+1000 to this.

On that note, I always congratulate people when they get their first
error message. Only way to learn is to fail first.

Karin

On 28/10/15 21:49, Sam Penrose wrote:
> I wonder if it is helpful in effect to reverse the polarity of the
> identification, to say:
>
> Programmers spend their time getting complex systems to play nicely,
> which is a process of repeatedly getting stuck, then making some
> progress, then getting stuck again. If you have felt stuck or
> bewildered at any point this morning, you were at that very moment
> programming. You are a programmer because you have already done what
> professional programmers do. Of course, we all try to work efficiently
> and make progress. You don't drive a Jeep for the purpose of breaking
> down in the back country, but we all recognize that the occasional
> breakdown is part of the journey. When you are sitting next to your
> Jeep and the big rock that broke its axle, you're not some phony
> armchair traveller in your living room. Even if its your first trip,
> you are a traveller. You are in the back country, with bugs and mud
> and, hopefully, beauty and accomplishment. When the message from the
> installer makes no sense at all, you're not a fraud. You are
> programming. So get help or make do, but don't feel like an impostor
> or a failure. You are a programmer doing your work, and you deserve
> respect for that -- especially from yourself.
>
> On Wed, Oct 28, 2015 at 1:24 PM, David Martin (Staff)
> <d.m.a.mar...@dundee.ac.uk> wrote:
>> What Karin says.
>>
>> Even in a less pressured environment there is no hope of someone turning up 
>> to a SC workshop and coming out of it a fully functioning and competent 
>> person int he areas they have been exposed to. However, what we have done, 
>> as instructors, is to sketch the route map and show how the concepts link 
>> together. The best students will spend 3x longer than the contact hours 
>> going back over it and learning the material thoroughly as they apply it.
>>
>> ..d
>>
>> Dr David Martin
>> Lecturer in Bioinformatics
>> College of Life Sciences
>> University of Dundee
>>
>>
>> 
>> From: Discuss <discuss-boun...@lists.software-carpentry.org> on behalf of 
>> Karin Lagesen <karin.lage...@gmail.com>
>> Sent: 28 October 2015 20:11
>> To: discuss@lists.software-carpentry.org
>> Subject: Re: [Discuss] pulling along those behind
>>
>> One of the things that I always emphasize before and during the workshop
>> is that my aim is not to teach them to be programmers, but to make it
>> less scary if and when they do decide to learn things more in depth. My
>> main goal is to demystify programming. That way, it becomes less about
>> understanding every detail and more about finding out that it is not as
>> complicated as it looks. I think that by doing that, even if I do lose
>> somebody on the little things, I manage to keep them with me on the
>> bigger, more conceptual things, if that makes sense.
>>
>> Karin
>>
>>
>> On 27/10/15 17:38, Bill Mills wrote:
>>> I stretch the skill-level bracket of all my workshops by leaning heavily
>>> on tiered challenge problems; I break for problems regularly (every 30
>>> minutes or so, giving those really struggling a chance to catch up), and
>>> set 'baseline' problems (that everyone is expected to solve) and
>>> 'stretch' goals - harder problems that the intermediates can derive
>>> value from.
>>>
>>> On Tue, Oct 27, 2015 at 9:33 AM, Noam Ross <noam.r...@gmail.com
>>> <mailto:noam.r...@gmail.com>> wrote:
>>>
>>>  One thing that I've found is that students who are behind sometimes
>>>  give up trying to type along and just read along with the lesson
>>>  notes.  While it's not

Re: [Discuss] undergrad curriculum examples

[David Martin (Staff)]

What are your contact hours and staff/student ratios like for that?

Part of our challenge is fitting it in to a curriculum that is already quite 
packed. We also have a challenge with different entry levels - students can 
start at level 1 or level 2. Then we have visiting students at level 3, 
students who spend level 2 elsewhere and return for level 3 and so on. Dealing 
with these cases in the context of assumed knowledge requires some care.

We will be spending more time on R/stats in the next year (up to 40 contact 
hours in level 2) so quite a large time investment. Preparing reports in R 
Markdown will definitely be on the agenda.

ggplot2 may still not be :)

My main SC like approach is in level 3 with an elective practical. This is 
typically small (6-10 students) and they are working 5 weeks half time (so 
nominally 20 hours/week) on that topic. I did try the first week as a SC crash 
course and then go back and use the bits to complete the project (wrap a set of 
data in a database with a python class that allows sensible questions to be 
asked of the data) but this was challenging - reading the chapter on frameworks 
in 'how learning works' made me realise that undergrads are far less well 
equipped to manage a broad complexity of topic than postgrads. We have to limit 
expectations and repeat more.

..d

From: Discuss [mailto:discuss-boun...@lists.software-carpentry.org] On Behalf 
Of Gorman, Gerard J
Sent: 22 April 2015 07:11
To: rfligh...@gmail.com
Cc: Software Carpentry Discussion
Subject: Re: [Discuss] undergrad curriculum examples

Hi Robert

For our 1st yr geoscience undergraduates we teach an introductory programming 
course with python (~90 students). The content is different from SC but we 
pretty much cloned all the teaching methodologies (thanks Greg!). Learning 
outcomes are much better than before and the student experience is good. We 
also did a workshop covering shell and git last year. This also went very well.

If you are taking on the fight to change the curriculum I have two pieces of 
advice. First pile up your evidence: lots of literature on what are good and 
bad first programming languages, what is the community using (do a survey if 
you have to), what is the competitor risk (i.e. everyone else is going to be 
kicking our ass if we don't do something), what are the teaching/research 
staff using (they can be good allies - project students etc). This will work 
with rational opposition. Irrational opposition is usually confined to one 
vocal person (lunatic) - but rather than waiting for them to retire you just 
work with everyone else to form a consensus. Scientists are usually pretty well 
behaved when you present evidence. If that fails then look for a job elsewhere 
;-)

Secondly, be stupidly well prepared if you do get your way. The first couple of 
years when I taught python it was pretty much a disaster mostly due to poor 
(traditional) teaching methodologies. I thoughts just switching from c++ to 
Python and being an enthusiastic teaching would be enough...it wasn't. And the 
fact is that you look pretty lame if you strongly advocate something and then 
blow it... Over time we made quite a few changes to improve the course but we 
only really nailed it after we did the SC instructor training ;-) One 
difference from SC is that for undergraduate teaching the classes can get much 
larger. The solution for this is an army of teaching assistants (in our case 
these are mostly grad students) which are familiar with SC.

Regards
Gerard

On 21 Apr 2015, at 22:59, David Martin (Staff) 
d.m.a.mar...@dundee.ac.ukmailto:d.m.a.mar...@dundee.ac.uk wrote:

Those look very interesting. We teach stats in RStudio from almost the minute 
they walk through the door in 1st year. We expect all graphs/representations to 
be literate and reports to demonstrate reproducibility through inclusion of the 
scripts. With a cohort of 200 (and rising) it is a challenge to embed those 
skills but by the time they get through to 3rd year they start to do some good 
stuff and are confident in large scale data wrangling.

Overheard in the library 'Why are you messing around with Excel? it is so much 
easier in R' from a cohort who are the antithesis of the nerdy geek programmer.

So we have successfully introduced R into the undergrad curriculum and are 
slowly training faculty who get a shock when the student in the genetics class 
ask for the raw data and do a proper ANOVA rather than the Fisher Price version 
the instructor had been doing for years because the student's didn't have the 
skills.

This amounts to about 5-6 contact hours in level 1 and substantially more (16+) 
in level 2. Level 1 covers basic plotting and descriptive stats. Level 2 covers 
statistical models, fitting and testing to multiway ANOVA.
We only teach the basic plots as I am not brave enough to attempt to teach 200 
18 year old biologists ggplot2 - their brains are too delicate.

I'm working on getting a reasonable

Re: [Discuss] undergrad curriculum examples

[David Martin (Staff)]

I have attempted this at our level 3 (level 4 is honours year).

It has some marginal success but there are limitations.


1) student skills and motivation. At a postgrad level students are much better 
prepared to take on the self learning that SC involves. They are also selected 
to be of the more able end of the curriculum.


2) background and time. A 2-day software carpentry workshop is comparable in 
learning delivery to a substantial chunk of a semester long course. It really 
doesn't go very far unless you are building on it with the appropriate 
repetition (which comes in naturally at postgrad level for the motivational 
reasons above) but is hard to do at undergrad where there are many other 
pressures working against you.

You also start with a background where they do not see the application and 
hence the motivation and take up is lower.


Having said that, for a certain cohort of students it would be an excellent 
opportunity.


Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee


From: Discuss discuss-boun...@lists.software-carpentry.org on behalf of 
Robert M. Flight rfligh...@gmail.com
Sent: 21 April 2015 18:43
To: Software Carpentry Discussion; Jennifer Bryan
Subject: [Discuss] undergrad curriculum examples

Does anyone know of any examples where software carpentry type skills have been 
integrated into an undergraduate science curriculum? It seems to me that the 
various skills taught in software carpentry could be integrated into an 
undergraduate science curriculum if done correctly, given the prevalence of 
data manipulations that are frequently performed in undergraduate science labs 
(chemistry titrations / conversions, physics equation fitting, biology number 
manipulations), at least in my experience over 10 years ago. I don't imagine 
that things have changed, and have likely gotten worse.

I know that Jenny Bryan is integrating a lot of this stuff into her advanced 
stats class (which is awesome), but the more I think about it, it seems that it 
would be useful to introduce things earlier rather than later.

I would be very appreciative if anyone has any specific examples from their own 
or others teaching.

Regards,

-Robert

Robert M Flight, PhD
Bioinformatics Research Associate
Resource Center for Stable Isotope Resolved Metabolomics
Markey Cancer Center
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.iohttp://rmflight.github.io
EM rfligh...@gmail.commailto:rfligh...@gmail.com
PH 502-509-1827

The most exciting phrase to hear in science, the one that heralds new 
discoveries, is not Eureka! (I found it!) but That's funny ... - Isaac 
Asimov


The University of Dundee is a registered Scottish Charity, No: SC015096
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[Discuss] Any one know someone who can help?

[David Martin (Staff)]

This is out of area for me, so I wonder if anyone closer could point this chap 
in the right direction.


http://www.linux.com/news/featured-blogs/200-libby-clark/813736-blind-genetics-researcher-wants-to-learn-linux-but-needs-a-tutor?

[http://www.linux.com/images/stories/41373/DNA-microarray.jpg]http://www.linux.com/news/featured-blogs/200-libby-clark/813736-blind-genetics-researcher-wants-to-learn-linux-but-needs-a-tutor

Blind Genetics Researcher Wants to Learn Linux But Needs a Tutor | Linux.com
Graduate student Thomas Hahn needs someone with sight - and Linux knowledge - 
to show him how to switch from Windows for his computational analysis.
Read 
more...http://www.linux.com/news/featured-blogs/200-libby-clark/813736-blind-genetics-researcher-wants-to-learn-linux-but-needs-a-tutor

I do know a blind informatician, but agin, on the wrong side of the pond.


..d


Dr David Martin
Lecturer in Bioinformatics
College of Life Sciences
University of Dundee


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Re: [Discuss] Python for biologists: Five things I hate about teaching Python

[David Martin (Staff)]

From: Discuss [mailto:discuss-boun...@lists.software-carpentry.org] On Behalf 
Of Lex Nederbragt
Sent: 03 March 2015 11:34
To: Software Carpentry Discussion
Subject: [Discuss] Python for biologists: Five things I hate about teaching 
Python

Hi,

I just found this post that some people may appreciate: 
http://pythonforbiologists.com/index.php/five-things-i-hate-about-teaching-python/

Lex

And as is typical it gets a load of programming solutions when what is needed 
are teaching solutions. Who thinks that inundating students with closures, 
context managers etc on their first day in dealing with programming is a good 
idea? Likewise 'just copy this, it is magic and will do what you want' is also 
deeply unsatisfactory.

..d

The University of Dundee is a registered Scottish Charity, No: SC015096
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