Re: [discuss] Is COVID-19 virus demanding alternative software carpentry workshop delivery options?

[Lex Nederbragt]

Our university is closed effective this evening, as are all others in Norway 
(and schools etc). We had already cancelled a planned Data Carpentry workshop, 
others sure will follow.

I think this resource “Pedagogy in times of disruption” from Stanford is really 
good: 
https://docs.google.com/document/d/1ccsudB2vwZ_GJYoKlFzGbtnmftGcXwCIwxzf-jkkoCU/preview#heading=h.ncz7vuwkudlv
 
<https://docs.google.com/document/d/1ccsudB2vwZ_GJYoKlFzGbtnmftGcXwCIwxzf-jkkoCU/preview#heading=h.ncz7vuwkudlv>


Lex

--
Dr. Lex Nederbragt
Centre for Bioinformatics and Dept. of Biosciences
University of Oslo
pronouns: he/him
Website lexnederbragt.com <http://lexnederbragt.com/>
Email lex.nederbr...@ibv.uio.no <mailto:lex.nederbr...@ibv.uio.no>




> On 12 Mar 2020, at 15:37, Clare Michaud via discuss 
>  wrote:
> 
> We’re cancelling two workshops scheduled for next week, and discussing 
> whether to virtually host some April workshops we have scheduled, at 
> UW-Madison. 
> 
> Clare
> ___
> Clare Michaud | she/her/hers
> Event and Communications Manager
> Data Science Hub <https://hub.datascience.wisc.edu/>
> University of Wisconsin-Madison
> cmich...@wisc.edu <mailto:cmich...@wisc.edu> | 608-316-4567
> 
>> On Mar 12, 2020, at 9:31 AM, Amy E. Hodge > <mailto:amyho...@stanford.edu>> wrote:
>> 
>> Workshops have definitely already been cancelled due to COVID-19, including 
>> one at Stanford in two weeks, and I expect there will be more cancellations 
>> in the future.
>>  
>> ~ Amy
>>  
>> Amy E. Hodge, PhD
>> Science Data Librarian
>> amyho...@stanford.edu <mailto:amyho...@stanford.edu>
>> 650.556.5194
>> Pronouns: she/her
>>  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: Olav Vahtras mailto:olav.vaht...@gmail.com>>
>> Reply-To: discuss > <mailto:discuss@lists.carpentries.org>>
>> Date: Thursday, March 12, 2020 at 1:27 AM
>> To: discuss > <mailto:discuss@lists.carpentries.org>>
>> Subject: Re: [discuss] Is COVID-19 virus demanding alternative software 
>> carpentry workshop delivery options?
>>  
>> Thanks Jason! 
>> AAPT has collected a large number of links  to online/remote teaching 
>> resources in this Google document:
>>  
>> https://docs.google.com/spreadsheets/d/1VT9oiNYPyiEsGHBoDKlwLlWAsWP58sGV7A3oIuEUG3k/edit#gid=1552188977
>>  
>> <https://docs.google.com/spreadsheets/d/1VT9oiNYPyiEsGHBoDKlwLlWAsWP58sGV7A3oIuEUG3k/edit#gid=1552188977>
>>  
>> Regards,
>> Olav
>>  
>> On Thu, Mar 12, 2020 at 9:02 AM arin_basu via discuss 
>> mailto:discuss@lists.carpentries.org>> wrote:
>>> Excellent thoughts Jason! 
>>> I am also thinking and planning to offer my dc-ecology workshop online as 
>>> well as in-person, so will see how it goes. Any thoughts or words to the 
>>> wise will be appreciated. 
>>> Best, 
>>> Arin
>>> 
>>> 
>>> Sent using Zoho Mail <https://www.zoho.com/mail/>
>>> 
>>>  On Thu, 12 Mar 2020 17:11:39 +1300 j.b...@cqu.edu.au 
>>> <mailto:j.b...@cqu.edu.au> wrote 
>>> 
>>>> G’day Software Carpentry colleagues
>>>>  
>>>> With the COVID-19 virus causing great concern, I am aware of a number of 
>>>> precautionary measures being applied globally to help reduce the spread of 
>>>> this virus.  Some of these measures include: events cancellation, travel 
>>>> bands, increase in workforce working from home or being placed in 
>>>> self-isolation, it is my personal opinion that this will have a flow on 
>>>> affect to software carpentry workshops.  I am not aware of any software 
>>>> carpentry workshops that have been cancelled because of this virus yet, 
>>>> but I believe that it is a matter of when, not if, that some workshops 
>>>> will be cancelled. 
>>>>  
>>>> With a desire to increase social distance of the general population, the 
>>>> interest in the use of virtual environments for training, presentations 
>>>> and general meetings it rising rapidly.  Because I believe strongly in 
>>>> what software carpentry is trying to achieve and I have personally seen my 
>>>> local participants benefitting from software carpentry workshops, I want 
>>>> to highlight m

Re: [discuss] Plotting and Programming with Python vs Programming with Python

[Lex Nederbragt]

Hi,

Greg Wilson is the one to answer, but here is my recollection of the history. 
(Apologies if I got that all wrong, Greg…)

"Programming with Python” 
 was built with a 
philosophy to get the learner to achieve something useful, in this case some 
visualisation, as early as possible in the lesson/workshop. Inspiration came 
from the Media Computation approach developed by Mark Guzdial (if I am not 
mistaken), see Porter et al: “Success in Introductory Programming: What Works?” 

 However, not many people know what that inflammation data is about, and many 
felt the approach did not work optimally - there is a lot of ‘magic' happening 
in the beginning - Numpy and Numpy arrays, 2D slicing and plotting all come in 
the first episode.
 
Greg then set out to develop a lesson that is more along the lines of ’teach 
concepts, and apply them, in an increasing order of complexity and usefulness’. 
This became "Plotting and Programming with Python” 
. See the design 
rationale here: http://swcarpentry.github.io/python-novice-gapminder/design/ 
. This lesson 
still needs some work to become fully mature (if I am not mistaken).

Hope that helps!

Lex



> On 21 May 2019, at 10:43, Valters, Declan A.  wrote:
> 
> Hi all,
>  
> Does anyone know the origin/philosophy behind the two separate Python core 
> lessons in the software carpentry workshops: i.e. "Programming with Python" 
> vs "Plotting and Programming with Python". Understand the latter is aimed at 
> Jupyter users specifically, and introduces Pandas early on rather the Numpy, 
> but it also has slightly different content in other ways too.
>  
> Or if anyone has experience in teaching both of them and can offer their 
> thoughts/feedback?
>  
> (Did spend some time searching the github issues and swc site to see if there 
> was any fundamental reason/motivation for having the two separate courses.)
>  
> Cheers,
> Declan
> 
> 
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Re: [discuss] CyVerse Foundational Open Science Skills Course - June 3-14, 2019, Tucson AZ

[Lex Nederbragt]

Hi Jason,

Is this workshop focussed on the US situation or would non-US PI’s benefit just 
as much?

Best,

Lex

> On 16 Apr 2019, at 19:31, Williams, Jason  wrote:
> 
> Hi Everyone,
> 
> We are running a two-week camp (attend one week or both) and I wanted to 
> spread the word about:
> 
> Foundational Open Science Skills (FOSS) is a novel, camp-style training 
> designed to prepare principal investigators and their lab teams, both new and 
> established, to meet the growing expectations of funding agencies, 
> publishers, and research institutions for scientific reproducibility and data 
> accessibility.
> 
> FOSS camp topics will include:
> • Cloud, HPC, and other computing technologies
> • Modern data science tools, platforms, and concepts, focusing on open source 
> resources
> • Analysis rigor, reproducibility, sharing, and collaboration across 
> institutional boundaries
> • Using open science resources for managing research projects
> • Metadata management skills for research discovery, integration, and reuse
> • Best practices to coordinate multidisciplinary science teams, ideas, and 
> scale analyses
> • Writing, critiquing, and implementing a data management plan to NSF-BIO 
> guidelines
>  • Creating and incubating an open science culture in your lab
> ​
> It will be at the University of Arizona (Tucson, AZ) June 3-14
> 
> We have waivers/scholarships available see more information here: 
> https://www.cyverse.org/foss
> 
> - Jason
> 
> P.S.  Materials aren’t up yet but will be open and available
> 
> --
> Jason Williams
> 
> Assistant Director, External Collaborations: DNALC
> Lead - Education, Outreach, Training: CyVerse
> DNA Learning Center
> Cold Spring Harbor Laboratory
> 1 Bungtown Rd.
> Cold Spring Harbor, NY 11724
> 516-367-5186 
> www.dnalc.org 
> 

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Re: [discuss] What's in a name: Live-Coding, or?

[Lex Nederbragt]

Hi all,

It pleases me to be able to say that after the next update of the instructor 
training materials, we will now refer to our teaching practice as 
'participatory live coding', where 'learners are strongly encouraged to 
"code-along" with the instructor.' (details in this pull request 
).

Thank you for these suggestions!

Best,

   Lex
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Re: [discuss] What's in a name: Live-Coding, or?

[Lex Nederbragt]

I like "One of the cornerstones of Software and Data Carpentry is our 
code-along method of teaching."

But I also like (inspired by David Martin) "One of the cornerstones of Software 
and Data Carpentry is participatory live coding" (or "our participatory live 
coding method of teaching").

The second maybe for more formal publications, and the first, with 
"code-alongs", for less formal occasions?

   Lex 

> On 22 Oct 2018, at 16:59, David Martin (Staff)  
> wrote:
> 
> participatory demonstration?
>  
> From: Lex Nederbragt [mailto:lex.nederbr...@ibv.uio.no] 
> Sent: 22 October 2018 3:22 PM
> To: Discuss list Carpentries 
> Subject: Re: [discuss] What's in a name: Live-Coding, or?
>  
> Thanks for the 'code-along' suggestion. I like it, it sounds great! However, 
> I am not sure how to use it in practice to describe our teaching method as it 
> seems to be meant as adjective, not a noun. For example, we currently write:
>  
> "One of the cornerstones of Software and Data Carpentry teaching is live 
> coding"
> 
> We can’t hardly change that to ‘is code-along’. We could use ‘is a code-along 
> style of interactive programming’, but that becomes too long again… ‘is 
> code-along sessions’ doesn’t work too well either. Oh, and ‘is code-along 
> live coding’ sounds weird.
>  
> So I like it as an adjective describing the style of teaching, but feel I’m 
> still looking for a better noun, or better adjective between ‘live’ and 
> ‘coding’.
>  
> Lex
> 
> 
> 
> On 15 Oct 2018, at 17:24, Hoyt, Peter  wrote:
>  
> +1
> 
> Peter Hoyt
> 
> On 10/15/2018 10:12 AM, Erin Becker wrote:
> I love code-along!
>  
> On Mon, Oct 15, 2018 at 5:19 AM Jeremy Metz via discuss 
>  wrote:
> +1 for code-along - short but descriptive, and also informal and fun sounding!
>  
> On Mon, 15 Oct 2018 at 13:04, Adriana De Palma  wrote:
> Code-along. As in sing-along. As in fun ☺
>  
> From: Lex Nederbragt [mailto:lex.nederbr...@ibv.uio.no] 
> Sent: 15 October 2018 12:49
> To: Discuss list Carpentries 
> Subject: [discuss] What's in a name: Live-Coding, or?
>  
> Hi,
>  
> I have for a while been thinking about the term ‘live-coding’ as we use it as 
> our teaching approach in workshops. What we mean is a form of teaching 
> described in the instructor training material as “work[ing] through the 
> lesson material, typing in the code or instructions, with the workshop 
> participants following along”. But there are other meanings of the term, for 
> example, some people will ‘live code’ a software demo during a conference, 
> without the participants doing any coding themselves. Apparently it even can 
> be done as a performing arts form (creating sounds, images, etc)- see the 
> wikipedia entry on ‘Live coding'.
>  
> I am looking for a term that better describes what we do. Examples I have 
> considered:
>  
> - live follow-along coding; however, follow-along does not imply learners 
> being active, they could just as well sit back, relax and follow along 
> closely (note that the description from the instructor training material uses 
> this wording also)
> - live interactive coding; however, there is not much interaction unless for 
> any truly interactive exercises
> - live together-coding or live collaborative coding; however, we are not 
> really coding together or collaboratively, learners merely mirror the 
> instructor (except for when they do exercises); still, these are currently my 
> favourites
>  
> Any other suggestions?
>  
> Best,
>  
> Lex
>  
>  
> 
>  
> --
> Associate Director, The Carpentries
> Pronouns: she/her/hers
>  
>  
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> The Carpentries / discuss / see discussions + participants + delivery options 
> Permalink

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Re: [discuss] What's in a name: Live-Coding, or?

[Lex Nederbragt]

Thanks for the 'code-along' suggestion. I like it, it sounds great! However, I 
am not sure how to use it in practice to describe our teaching method as it 
seems to be meant as adjective, not a noun. For example, we currently write:

"One of the cornerstones of Software and Data Carpentry teaching is live coding"

We can’t hardly change that to ‘is code-along’. We could use ‘is a code-along 
style of interactive programming’, but that becomes too long again… ‘is 
code-along sessions’ doesn’t work too well either. Oh, and ‘is code-along live 
coding’ sounds weird.

So I like it as an adjective describing the style of teaching, but feel I’m 
still looking for a better noun, or better adjective between ‘live’ and 
‘coding’.

Lex


> On 15 Oct 2018, at 17:24, Hoyt, Peter  wrote:
> 
> +1
> 
> Peter Hoyt
> 
> On 10/15/2018 10:12 AM, Erin Becker wrote:
>> I love code-along!
>> 
>> On Mon, Oct 15, 2018 at 5:19 AM Jeremy Metz via discuss 
>> mailto:discuss@lists.carpentries.org>> wrote:
>> +1 for code-along - short but descriptive, and also informal and fun 
>> sounding!
>> 
>> On Mon, 15 Oct 2018 at 13:04, Adriana De Palma > <mailto:a.de-pa...@nhm.ac.uk>> wrote:
>> Code-along. As in sing-along. As in fun ☺
>> 
>>   <>
>> From: Lex Nederbragt [mailto:lex.nederbr...@ibv.uio.no 
>> <mailto:lex.nederbr...@ibv.uio.no>] 
>> Sent: 15 October 2018 12:49
>> To: Discuss list Carpentries > <mailto:discuss@lists.carpentries.org>>
>> Subject: [discuss] What's in a name: Live-Coding, or?
>> 
>>  
>> Hi,
>> 
>>  
>> I have for a while been thinking about the term ‘live-coding’ as we use it 
>> as our teaching approach in workshops. What we mean is a form of teaching 
>> described in the instructor training material 
>> <https://carpentries.github.io/instructor-training/15-live/index.html> as 
>> “work[ing] through the lesson material, typing in the code or instructions, 
>> with the workshop participants following along”. But there are other 
>> meanings of the term, for example, some people will ‘live code’ a software 
>> demo during a conference, without the participants doing any coding 
>> themselves. Apparently it even can be done as a performing arts form 
>> (creating sounds, images, etc)- see the wikipedia entry on ‘Live coding'.
>> 
>>  
>> I am looking for a term that better describes what we do. Examples I have 
>> considered:
>> 
>>  
>> - live follow-along coding; however, follow-along does not imply learners 
>> being active, they could just as well sit back, relax and follow along 
>> closely (note that the description from the instructor training material 
>> uses this wording also)
>> 
>> - live interactive coding; however, there is not much interaction unless for 
>> any truly interactive exercises
>> 
>> - live together-coding or live collaborative coding; however, we are not 
>> really coding together or collaboratively, learners merely mirror the 
>> instructor (except for when they do exercises); still, these are currently 
>> my favourites
>> 
>>  
>> Any other suggestions?
>> 
>>  
>> Best,
>> 
>>  
>> Lex
>> 
>>  
>>  
>> 
>> 
>> -- 
>> Associate Director, The Carpentries
>> Pronouns: she/her/hers
> 
> The Carpentries <https://carpentries.topicbox.com/latest> / discuss / see 
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[discuss] What's in a name: Live-Coding, or?

[Lex Nederbragt]

Hi,

I have for a while been thinking about the term ‘live-coding’ as we use it as 
our teaching approach in workshops. What we mean is a form of teaching 
described in the instructor training material 
 as 
“work[ing] through the lesson material, typing in the code or instructions, 
with the workshop participants following along”. But there are other meanings 
of the term, for example, some people will ‘live code’ a software demo during a 
conference, without the participants doing any coding themselves. Apparently it 
even can be done as a performing arts form (creating sounds, images, etc)- see 
the wikipedia entry on ‘Live coding'.

I am looking for a term that better describes what we do. Examples I have 
considered:

- live follow-along coding; however, follow-along does not imply learners being 
active, they could just as well sit back, relax and follow along closely (note 
that the description from the instructor training material uses this wording 
also)
- live interactive coding; however, there is not much interaction unless for 
any truly interactive exercises
- live together-coding or live collaborative coding; however, we are not really 
coding together or collaboratively, learners merely mirror the instructor 
(except for when they do exercises); still, these are currently my favourites

Any other suggestions?

Best,

Lex



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Re: [discuss] How can we scale up Carpentries training at universities?

[Lex Nederbragt]

Hi again,

Thank you so much for your thoughtful and many responses. I have tried to copy 
the main points for each answer in a google doc, and I thought why not share it 
with you  
<https://docs.google.com/document/d/1_DiXTLo6StFaINTZHvZmiWpu7D7rfgVuI-iFMLk8EB8/edit?usp=sharing>in
 case someone finds it interesting.

There are definitely many ways to scale up Carpentry activities at universities 
and there does not seem to be a one-model-fits-all. Many commented the 
differences between semester-long courses and short intensive workshops, where 
the long courses allow a slower tempo with more reflection, a different dynamic 
and learner (and teacher) motivation. There were good suggestions to mitigate 
these effects and/or adjust the teaching/curriculum. And this is the take-home 
message for me: use what works from the Carpentries, try to use certified 
instructors as much as you can (as teachers and assistants), adjust the 
material and setting to so it can be scaled.

One specific response: David Martin asked

>  I am very keen to see how Lex has got on with his databeregning 101 module 
> in Oslo.

He is referring to the course 'Introduction to Computational Modelling for the 
Biosciences” ​that I am developing and teaching here in Oslo (see my blog post 
about the first edition 
<https://flxlexblog.wordpress.com/2017/12/21/experiences-with-the-first-edition-of-introduction-to-computational-modelling-for-the-biosciences/>).
 Reflecting on your responses - forgive my for blowing my own horn a bit - it 
appears I am already following many of your suggestions: this year, we use 
live-coding as main teaching method for programming, I have the assistants go 
through parts of the Carpentries instructor training curriculum, especially 
those that will do the live-coding. And it seems to work - at least students 
and assistants are very content (we do need to check whether learning actually 
take place :-) ).

In summary, I think we will try two different approaches: 
- increasing the offering of intense, one-day and two-day workshops, aiming to 
give credit to learners and make it worthwhile for the instructors and 
tailoring (parts of it) to specific research domains
- ‘carpentrify’ the master (and sometimes also bachelor) curriculum towards 
semester-long courses where skill development is a central point (I have to 
mention the “Data Carpentry for Biologists 
<http://datacarpentry.org/semester-biology/nav/about/>” effort from the 
University of Florida as a successful example), including instructor training 
(TA’s and professors!), incorporating all that works well and tailoring it to 
regular university courses.

Regards,

Lex Nederbragt
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[discuss] How can we scale up Carpentries training at universities?

[Lex Nederbragt]

Hi community,

At the University of Oslo (UiO), we have an ongoing process that will result in 
a Masterplan for IT at the university. I am part of the task force responsible 
for writing this plan, and have been tasked to contribute to a section on 
skills training. We have a large Carpentries effort at UiO, regularly teaching 
one-day workshops with one lesson of the Software Carpentry stack each 
(including make and testing/continuous integration), very popular two-day R 
(tidyverse), and occasionally Data or Library Carpentry lessons or full two-day 
workshops. Many at UiO are now seeing the need to offer this kind of skills 
training more widely and organized as formal course offerings, potentially with 
students earning credit. 

I am very happy with this development as it is a recognition of the skill gap 
that exists amongst researchers, and a testament to the success of The 
Carpentries and our local effort in filling it. However, I also worry that we 
may lose something in the process of scaling up offering these workshops.

By making Carpentry workshops a core offering across departments, with students 
able to earn credit from them, my fear is that the spirit of the volunteer 
effort gets lost or may become reduced. Making our workshops into required 
courses may change (reduce) the motivation for learners and instructors.

So here are my questions to you:

   ⁃Have other universities made the same move, or are they planning this, 
and if so, how are they organizing this effort?
   ⁃How to keep learners motivated if they feel they are required to take a 
Carpentries workshops?
   ⁃How to keep the quality of instruction, and instructor motivation, 
high, if workshops become organized like regular courses?

I’d appreciate any suggestions that will help us become succesful scaling up 
our Carpentries skills training!

Regards,

 Lex Nederbragt


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[discuss] Position as Associate Professor of Bioinformatics, University of Oslo

[Lex Nederbragt]

Hi,

At the University of Oslo we have started a Centre for Bioinformatics, to which 
I am connected. As part of this move, we are able to announce a new position as 
Associate Professor in Bioinformatics. This person will work at both the 
Department of Biosciences and the new Centre for Bioinformatics.

As this new centre will also set up an education and training program (part of 
my job), this position would be an excellent match for a Carpentries instructor!

Details: 
https://www.jobbnorge.no/en/available-jobs/job/156323/associate-professor-in-bioinformatics.
 Don’t hesitate to contact me if you have any questions!

Best,

Lex Nederbragt

--
Lex Nederbragt
Centre for Bioinformatics and Dept. of Biosciences
University of Oslo
P.O. Box 1066 Blindern 0316 Oslo, Norway
Ph. +47 22844132 +47 48028722
Email lex.nederbr...@ibv.uio.no <mailto:lex.nederbr...@ibv.uio.no>

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Re: [discuss] Knowing what lessons will be delivered at a workshop

[Lex Nederbragt]

Hi,

Thanks for bringing this up. The Executive Council (of which I am a member) is 
aware of this issue and is actually discussing it internally, and we will reach 
out to the community for input as well. By the way, relational databases are no 
longer part of the ‘branded’ Software Carpentry workshops, while the shell, 
version control and a programming language are.

Best,

Lex Nederbragt.

> On 8 Aug 2018, at 02:36, Ben Bolker via discuss 
>  wrote:
> 
> 
>  This is an understandable, and difficult, tension.
> 
>  I thought relational DBs were part of Data Carpentry more than SC? It
> was my understanding that VC/shell/programming language were *required*
> components of a SC workshop, although obviously people will bend the
> rules ...
> 
> 
> On 2018-08-07 07:23 PM, Jason Moore via discuss wrote:
>> Hi,
>> 
>> For a number of years, software carpentry would teach 4 things at every
>> workshop: version control, shell, relational databases, and a
>> programming language intro. There were some options, like git vs
>> mercurial or r vs matlab vs python, but if you went to a workshop you'd
>> get these 4 skills.
>> 
>> This was quite convenient because I knew if I sent my new students to
>> the latest nearby workshop they'd come back with those basic building
>> blocks in place and could start working with my group on projects.
>> 
>> Now, I see announcements of new workshops nearby and get excited to let
>> my new students know about them, but once I look closer the lessons are
>> all over the place. In fact, I've seen few recently that hit the SWC 4
>> skills and I really really want my students to get those under their
>> belt as a foundation. I've resorted to sending them to videos of those
>> lessons instead.
>> 
>> The diversity in lessons is great in one aspect, but we never really
>> know what we are going to get. The consistency of SWC lessons had many
>> advantages and I didn't care much whether the students learned git or
>> mercurial or any of the difference languages, only that they got those 4
>> skills.
>> 
>> Anyone else have this thought? And if so, are there any ideas for
>> improvement?
>> 
>> Jason
>> moorepants.info <http://moorepants.info/> <http://moorepants.info 
>> <http://moorepants.info/>>
>> +01 530-601-9791
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