Re: [Discuss] introduction to SWC

[Peter Steinbach]

Dear Stefan,

I am pasting a message by jonah that he sent me the other. the materials 
are all open and public, so I am not giving away any secrets (@Jonah 
just wanted to spare you the typing):

--
Peter,

There is a lot of good information around. We're trying to get better and
bringing it together in ways that are useful to members.

Slides I typically use are here:
https://www.slideshare.net/jduckles/software-carpentry-data-carpentry

Software Carpentry Survey report:
https://carpentries.github.io/assessment/software-carpentry/postworkshop/2017-July/swc_postworkshop_report_July2017.html

Long-term follow up survey report:
https://carpentries.github.io/assessment/long-term-survey/2018-January/2018_January_long_term_report.html

There is also a very good report on why instructors teach for us and the
benefits they get by doing so. In the last section it even has some of the
"ugly" (albeit not really that ugly) you are looking for.
https://software-carpentry.org/files/bib/duckles-instructor-engagement-2016.pdf

Hope that all helps! Let me know if there are other angles you were hoping
for and I'll see what we have.

Regards,
---
Jonah Duckles
Software Carpentry, Executive Director
http://software-carpentry.org

I have found this material very useful.

Best,
Peter

On 03/19/2018 02:12 AM, Rayna Harris wrote:

I was asked for the same thing yesterday. I found this 90-second
presentation <https://www.youtube.com/watch?v=AHt3mgViyCs> by Greg, but its
a bit outdated being from 2012.

I might have to make my own 60-second video in Spanish, but it would be
nice to know what short videos in English are out there.

Rayna

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

On Fri, Mar 16, 2018 at 6:55 AM, Stefan Lüdtke <slued...@gfz-potsdam.de>
wrote:


Hi there,

I am wondering whether there is 2 minutes presentation around to introduce
SWC
at a meeting and do a bit of advertisement?

Cheers,

Stefan

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss



I was asked for the same thing yesterday. I found this 90-second 
presentation <https://www.youtube.com/watch?v=AHt3mgViyCs> by Greg, 
but its a bit outdated being from 2012.


I might have to make my own 60-second video in Spanish, but it would 
be nice to know what short videos in English are out there.


Rayna

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

On Fri, Mar 16, 2018 at 6:55 AM, Stefan Lüdtke 
<slued...@gfz-potsdam.de <mailto:slued...@gfz-potsdam.de>> wrote:


Hi there,

I am wondering whether there is 2 minutes presentation around to
introduce SWC
at a meeting and do a bit of advertisement?

Cheers,

Stefan

___
Discuss mailing list
Discuss@lists.software-carpentry.org
<mailto:Discuss@lists.software-carpentry.org>
http://lists.software-carpentry.org/listinfo/discuss
<http://lists.software-carpentry.org/listinfo/discuss>




___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss


--
Peter Steinbach, Dr. rer. nat.
Scientific Software Engineer, Scientific Computing Facility

Scionics Computer Innovation GmbH
Löscherstr. 16
01309 Dresden
Germany

phone +49 351 210 2882
fax   +49 351 202 707 04
www.scionics.de

Sitz der Gesellschaft: Dresden (Main office)
Amtsgericht - Registergericht: Dresden HRB 20337 (Commercial Registry)
Ust-IdNr.: DE813263791 (VAT ID Number)
Geschäftsführer: John Duperon, Jeff Oegema (Managing Directors)
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

[Discuss] inverted carpentries?

[Peter Steinbach]

Hi to all,

I was discussing the idea of an "inverted class room" teaching approach 
with a friend of mine who is a high school teacher (he uses that based 
on video recordings for his students ... just awesome AFAIK). I was 
hence wondering, if people have tried to teach the carpentry lessons in 
this way?


This would mean, that I record some of the parts of a carpentry lesson 
in video(s) (10-15 minute each) and ask the students to watch these 
videos before the carpentry bootcamp! The in-presence part of the 
workshop is then used to do exercises and try to fortify the content of 
the videos.


For me the biggest advantage of this approach is, that each learner can 
overcome the initial steep learning curve given their own speed of 
learning - which is a constant source of trouble when I teach.


Looking forward to your feedback -
Peter

--
Peter Steinbach, Dr. rer. nat.
Scientific Software Engineer, Scientific Computing Facility

Scionics Computer Innovation GmbH
Löscherstr. 16
01309 Dresden
Germany

phone +49 351 210 2882
fax   +49 351 202 707 04
www.scionics.de

Sitz der Gesellschaft: Dresden (Main office)
Amtsgericht - Registergericht: Dresden HRB 20337 (Commercial Registry)
Ust-IdNr.: DE813263791 (VAT ID Number)
Geschäftsführer: John Duperon, Jeff Oegema (Managing Directors)
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

[Discuss] open hackathon for porting your application to GPUs

[Peter Steinbach]

Dear fellow carpenters,

there are still free spots in the upcoming GPU Hackathon in Dresden 
(Germany) which is held in collaboration with FZ Juelich (Germany)

and the Oak Ridge Leadership Compute Facility (USA).

If you are thinking about porting your application to GPUs or improving 
your existing GPU application, you can receive one week of free 
consulting from experts while working on your own code.


Apply here:
https://www.olcf.ornl.gov/training-event/2018-gpu-hackathons/
until Jan 19!

Feel free to forward this message to anyone interested,
Peter

--
Peter Steinbach, Dr. rer. nat.
Scientific Software Engineer, Scientific Computing Facility

Scionics Computer Innovation GmbH
Löscherstr. 16
01309 Dresden
Germany

phone +49 351 210 2882
fax   +49 351 202 707 04
www.scionics.de

Sitz der Gesellschaft: Dresden (Main office)
Amtsgericht - Registergericht: Dresden HRB 20337 (Commercial Registry)
Ust-IdNr.: DE813263791 (VAT ID Number)
Geschäftsführer: John Duperon, Jeff Oegema (Managing Directors)
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

Re: [Discuss] Serverless scientific computing (function as a service)

[Peter Steinbach]

Hi everyone,

thanks for the interesting discussion so far. From my personal point of 
view, I'd fully agree with the computational burst based argument. If a 
robust pipeline needs to scale for a short amount of time and local HPC 
resources are blocked, the cloud is an essential resource.


However, with projects like [1] or [2] I don't buy into the argument 
that using HPC is forbidding due to reproducibility of scientific 
results. I know that many HPC installations are very conservative when 
it comes to containerized execution (like in the cloud) and have a long 
lag of implementing modern technologies, but containerized execution for 
the sake of having a fixed set of dependencies can also be considered as 
a lack of software quality. For me, this in turn is as a result of our 
academic system of incentives, i.e. published results are valued higher 
than the tools that produced them (which makes people invest less in 
infrastructure). The latter often leads to brittle build systems and the 
lack of tests. It's interesting (if not paradox) to me that people tend 
to take money in their hands to buy compute hours in the cloud to 
actually mitigate this.


Cheers,
Peter

[1] http://www.nersc.gov/research-and-development/user-defined-images/
[2] http://singularity.lbl.gov/


On 06/13/2017 08:12 PM, C. Titus Brown wrote:

Hi all,

we have done varying amounts of cloud computing, but it tends not be
price competitive when developing/debugging analysis pipelines for large
sets of data (vertebrate GWAS, etc.) because of the disk space needs.

The UCSC Genome Center folk are relying increasingly on cloud computing
because it is so flexible and burst-scalable - also see Dockstore.org
for something that they are doing across cancer centers.

With regard to Alex Savio's comment on clinical data -  I don't know where in
the world you are, Alex, but at least in the US there are several portions of
AWS that are HIPAA-compliant.  The entire UC system can use AWS for clinical
data now, for example.  I can seek out details if anyone is interested.

Personally I think HPCs are a problem for reproducibility (see
blogs.nature.com/naturejobs/2017/06/01/techblog-c-titus-brown-predicting-the-paper-of-the-future)
 for a small bit of context and am a big fan of
computing *like* you're in the cloud (VMs or docker or singularity) so as to
manage dependencies. But while that is something that quite a few experienced
computational folk seem to agree with, I'm not sure how many people I will be
able to convince of that in the broader world ;).

best,
--titus

On Tue, Jun 13, 2017 at 05:54:36PM +, alexsa...@gmail.com wrote:

Hi Peter,

I wouldnt be able to use such services with clinical data. It's totally not
an option for me.
Although I've seen some talks and the performance seems quite competitive
since scalability is easy. It's true that uploading a big quantity of data
can take a considerable time and bandwith, some labs use the weekends for
data uploading. One problem may be to convince University fund managers to
pay for external computing services when they already provide HPC services.

My five cents...

On Tue, 13 Jun 2017, 13:38 Peter Steinbach, <steinb...@scionics.de> wrote:


Dear both,

as a side note (and my apologies for digressing), I was wondering how
popular cloud computing for data processing at scale in an academic
context is in the US or elsewhere?

Here in Europe, many universities run their own HPC centers where people
can sign up to process larger amounts of data or do larger simulations
or whatnot ... mostly people here are concerned about efficiency (data
connnections into the cloud are typically poor, VM overhead is
considerable) and security/confidentiality when putting scientific
workflows into the cloud.
What is your take on this?

Best,
Peter


PS. I love the "serverless" metaphor. Get's rid of all the problems of
computers. ;)

On 06/12/2017 06:02 PM, Marianne Corvellec wrote:

Hi Justin,

Thank you so much for the quick reply!

I'm going to give this new package a try.

Best,
Marianne

On Fri, Jun 9, 2017 at 11:20 AM, Justin Kitzes <jkit...@berkeley.edu>

wrote:

Hi Marianne,

PyWren by Eric Jonas sounds like it's pretty similar to what you're

looking for -


http://pywren.io/

It's a relatively new package that's still in active development, but

Eric is very interested in expanding it (and has some support from the
riselab at UC Berkeley to do so). I know that he's also actively looking
for use cases, so I'd definitely suggest getting in touch with him if
you're interested.


Best,

Justin

--
Justin Kitzes
Energy and Resources Group
Berkeley Institute for Data Science
University of California, Berkeley


On Jun 9, 2017, at 6:51 AM, Marianne Corvellec <

marianne.corvel...@gmail.com> wrote:


Dear community,

I'm curious as to whether some of you might have worked on or used
solutions such as AWS Lambda in the context of your scientific
research.

If so, have

Re: [Discuss] Serverless scientific computing (function as a service)

[Peter Steinbach]

Dear both,

as a side note (and my apologies for digressing), I was wondering how 
popular cloud computing for data processing at scale in an academic 
context is in the US or elsewhere?


Here in Europe, many universities run their own HPC centers where people 
can sign up to process larger amounts of data or do larger simulations 
or whatnot ... mostly people here are concerned about efficiency (data 
connnections into the cloud are typically poor, VM overhead is 
considerable) and security/confidentiality when putting scientific 
workflows into the cloud.

What is your take on this?

Best,
Peter


PS. I love the "serverless" metaphor. Get's rid of all the problems of 
computers. ;)


On 06/12/2017 06:02 PM, Marianne Corvellec wrote:

Hi Justin,

Thank you so much for the quick reply!

I'm going to give this new package a try.

Best,
Marianne

On Fri, Jun 9, 2017 at 11:20 AM, Justin Kitzes  wrote:

Hi Marianne,

PyWren by Eric Jonas sounds like it's pretty similar to what you're looking for 
-

http://pywren.io/

It's a relatively new package that's still in active development, but Eric is 
very interested in expanding it (and has some support from the riselab at UC 
Berkeley to do so). I know that he's also actively looking for use cases, so 
I'd definitely suggest getting in touch with him if you're interested.

Best,

Justin

--
Justin Kitzes
Energy and Resources Group
Berkeley Institute for Data Science
University of California, Berkeley


On Jun 9, 2017, at 6:51 AM, Marianne Corvellec  
wrote:

Dear community,

I'm curious as to whether some of you might have worked on or used
solutions such as AWS Lambda in the context of your scientific
research.

If so, have you documented it in a blog post that you could share?
Thanks in advance!

Without even considering workflows or full-fledged projects, wouldn't
we want to be able to make a standard API call to, say, fit a
polynomial to some data?  Is anyone aware of any effort in this
direction?

A friend of mine just drew my attention to this general issue, which
touches on open science and reproducible research...  In the meantime,
I'll encourage him to join this mailing list!

Thank you,
Marianne
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss



___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss


___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

Re: [Discuss] Cool book on Python --> Numpy

[Peter Steinbach]

this looks really good, +1 for sharing
thanks!
P

On 01/16/2017 08:37 AM, Kunal Marwaha wrote:

I know it's a crowded field, but I really like this book. Perhaps other in
the SWC community would enjoy it too.

http://www.labri.fr/perso/nrougier/from-python-to-numpy/


___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

Re: [Discuss] hpc-novice revival?

[Peter Steinbach]

Dear list,

I have submitted a PR
https://github.com/swcarpentry/hpc-novice/pull/9

containing a possible outline of the contents in the course.
https://github.com/psteinb/hpc-novice/blob/9a584e9fe0fa1009e0cc32228684ca1685038364/outline.md

Best,
Peter
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

Re: [Discuss] hpc-novice revival?

[Peter Steinbach]

Dear Anelda,

thank you for your reply. I think we have to go through the discussion 
again about what should this lesson contain that you bring up. In nuce, 
I think we should concentrate on 1-2 core principles behind cloud and 
hpc. I agree that many scientists are confused by the availability of 
computing resources today. Therefor, I had in mind teaching HPC 
(classical simulations) versus HTC (a majority of bioinformatics, image 
processing, deep learning, cloud stuff) based on a somewhat simple 
example without diving too much into the details of the underlying APIs. 
With this, I hope to convey a simple mental model that will help 
participants not only to exploit HPC/cloud more effectively but also to 
judge available technologies better.


I warmly invite you to repost your reply in a contrived manner here:
https://github.com/swcarpentry/hpc-novice/issues

Best,
Peter

On 06.12.2016 04:54, ane...@talarify.co.za wrote:

Dear Peter,

Seems like HPC Carpentry crops up at least every 2 months in 
conversations around the world.


We recently had a great email chat between Mateusz Kuzak (Netherlands 
eScience Centre), Christina Koch (University of Wisconsin-Madison), 
Peter van Heusden (South African National Bioinformatics Institute) 
and myself.


We would ideally like to see a lesson on research computing 
infrastructure - explaining the different infrastructures that are 
available - grid, cloud, hpc, other(?) and helping researchers to 
understand when to use what - or rather what they need to address 
their specific research computing needs. This is more than just HPC 
novice, but with such a wide variety of infrastructures becoming very 
accessible (even to researchers in Africa) it would be great if our 
researchers understood why they should/could use the one or the other.


Once we have a lesson like this in place, an applied HPC lesson might 
have much more impact? I'd love to see a HPC novice lesson developed 
to complement that as our university (and I suppose many around South 
Africa) could benefit greatly from it.  Previously people have bumped 
into the problem of HPCs which are differently configured, but I think 
there is a sufficient level of abstraction possible where novices can 
learn concepts applicable to HPC in the broad even if they were taught 
the details of a specific system. Learning the new vocabulary of 
queues, head nodes, schedulers, etc will already take them a long way 
in being able to talk to their HPC service provider.


I'm not sure how far things have gone with the lesson I describe above 
- I think Christina and possibly Mateusz was working on something to 
this effect?


Happy to be involved in both.

By chance I'll be at the South African HPC conference this week and 
could see if there is interest there to help develop?


Kind regards,

Anelda


___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

Re: [Discuss] Python intermediate? First time teaching? Core curriculum?

[Peter Steinbach]

Dear Davide,

besides the administrative issues, I'd be curious to know what topics 
you would be up to? And what your target audience is?


Currently, python-intermediate-mosquitoes targets mostly modularisation 
(which should/could/must be split up and the overarching storyline needs 
more thinking, I feel), defensive programming (which should/could/must 
be extended IMHO) and concurrency (which in my opinion requires 
extensive cleaning).


I am happy to support you as I think that intermediate material is 
definitely missing in the SWC curriculum.


Best,
Peter

On 04/05/2016 04:47 AM, Davide Del Vento wrote:

I have questions about the python intermediate lessons, and the first
time teachings.

At the moment there are two repos, namely

https://github.com/swcarpentry/python-intermediate (empty!!)

and

https://github.com/swcarpentry/python-intermediate-mosquitoes (which
says to see https://github.com/swcarpentry/lesson-template for
instructions on formatting, building, and submitting lessons, but the
only instructions I could find are
https://github.com/swcarpentry/lesson-template/blob/gh-pages/CONTRIBUTING.md
and don't say much)

Now, I (~= NCAR) need(s) a python-intermediate-geospatial or something
like that. I'll be happy to develop that, and I was wondering the best
way to proceed. One way could be to fork the mosquitoes lesson, which
is a pretty good start for my purpose. Is that ok? If so, does it
matter if I do it as myself or as NCAR (which is a github org which I
can create projects in)? If I proceed that way, how will the eventual
transfer to swcarpentry org happen? Or should I do something
different?

Note also, that I may need to teach this class (few days long)
sometimes next summer and that I haven't completed the checkout yet
(but I taught similar python classes in the past as non--SWC). Is it
realistic to be ready this way? IIRC as newbie instructor, I should be
assisted by other non-newbies in my first teachings, but of course
nobody will be already familiar with the material. So how do new
lessons get "bootstrapped"? Alternatively, I can get another NCAR SWC
instructor (still not checked out yet), who is familiar with the
material. That would be two newbies, is it acceptable?

Any other suggestions? I will be ok to teach the material as non-SWC
for this time, as last resort. Actually this "last resort" may still
be the best, since we just taught git to the audience for this python
class (non-SWC since we weren't ready to do it that way), and they
already are proficient enough in shell (which actually they are
deprecating, in favor or using python, maybe with plumbum, for
everything, not only the geospatial stuff), so they would not be
interested in git or shell. So, are there exceptions to the "must
cover the core of Software Carpentry's curriculum" rule?

Thanks,
Davide
PS: boy that's way more than I had in mind for this message, I kept
adding to the subject... Feel free to split the answers under 3
separate conversations, if appropriate.

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org



___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

Re: [Discuss] scientific computing, HPC and tests

[Peter Steinbach]

hi guys,

I'd sign off of both Davide's and Trevor's arguments - thanks for the 
reconfirmation. And I do agree with Trevor, that teaching people TDD 
that have never bumped their head against the wall because of a bug they 
cannot find, is ambitious. I believe it's the same with version control 
(without wanting to start a discussion about it here). People that just 
have small scripts that they use occasionally, don't pick up git from 
our bootcamps because they don't have to in terms of their day-to-day 
needs. Once they really swallowed a bitter pill, they potentially start 
adopting. It's hard to do anything about it, I guess, besides being a 
role model and giving emotional lessons/trainings about it. ;)


Best,
P

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

Re: [Discuss] scientific computing, HPC and tests

[Peter Steinbach]

Dear Ashwin,

On 03/09/2016 01:15 PM, Ashwin Trikuta Srinath wrote:

Hi Peter - great post(s)! In case you haven't seen them already, lot of
great arguments have been made here [1] about why teaching testing may/may
not be a good idea in our workshops.


Yes, I read this post a long time ago. And I know that Greg initiated a 
project on testing but that didn't receive too much attention. Correct 
me if I am wrong.




I'm in favour of teaching testing - even if it is in the style of the
regression tests you mentioned. But I'm not so sure about unit tests, or
even if application code built on libraries can/should be "unit" tested.


Well, I would very emotionally start arguing against this. As unit tests 
are my day-to-day tool that I use for application and for library code 
and they have rescued my !*&^% multiple times. As most of my tasks 
involve accelerating applications, I always say no speed-up is of use if 
the results are wrong.

But maybe I don't see your point, can you please elaborate!



Can you give us some examples of the type of unit tests that you found? Did
you see a "theme" in the unit tests presented by both groups?

[1]


Not really, I know that the planet hunters basically had a pipeline to 
go through for each image (or data set) they wanted to process. I think 
they wrote unit tests for each step. For the others, I cannot say. I am 
currently waiting for more material from the hackathon to come online. 
If you want, I can provide a follow up as I am intrigued by this 
question as well.


Best,
P

--
Peter Steinbach, Dr. rer. nat.
Scientific Software Engineer, Scientific Computing Facility

Scionics Computer Innovation GmbH
Löscherstr. 16
01309 Dresden
Germany

phone +49 351 210 2882
fax   +49 351 202 707 04
www.scionics.de

Sitz der Gesellschaft: Dresden (Main office)
Amtsgericht - Registergericht: Dresden HRB 20337 (Commercial Registry)
Ust-IdNr.: DE813263791 (VAT ID Number)
Geschäftsführer: John Duperon, Jeff Oegema (Managing Directors)

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

[Discuss] scientific computing, HPC and tests

[Peter Steinbach]

Hi to all,

I just wanted to share some insights that I made during a GPU focused 
hackathon last week. For the full glory of details, see a series of blog 
posts on Eurohack 2016 in Dresden (Germany):

https://gcoe-dresden.de/?page_id=4

The hackathon had 6 teams come into Dresden with their HPC codes. The 
goal was to accelerate the apps to run on GPUs using a more recent 
programming paradigm called OpenACC as well as traditional CUDA. The 
codes were from weather forecasting (CFD based), simulating rescue paths 
for fire fighters in underground stations (also CFD based), correlating 
genomics with neuron activity (a matlab port), polymer simulation, 
bacteria simulation and planet hunting in interferrometric astronomy 
data (python based).


First observation, 2 out of 6 teams came with unit tests at all! The 
team I mentored had a minimal test tool that compared the ascii output 
of a simulation run with some reference output - so something on the 
level of an integration test with the full application.
We spent 2 days trying to understand the code and hunting bugs in an 
existing GPU based execution path which gave different results than the 
legacy CPU part. As we only had integration style tests, this was a 
tedious process as the code base was ~70 kloc large. At some point we 
ditched the existing GPU implementation and started from scratch.
I have to say that my team was very open to new ideas and promised to 
look into unit testing and the like, we didn't have time to refactor the 
code to become (unit) testable. If they'll do it, I don't know as it 
depends mostly on social factors.


Bottom line for SWC: defensive programming and testing are important and 
we should try to keep it in the curriculum as much as possible. My team 
were 3 meteorologists that received introductory level fortran training 
during their studies - nothing more.


Best,
Peter

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

Re: [Discuss] further reading

[Peter Steinbach]

Dear all,

thank you for all the replies. I think this is a somewhat tricky task. I still 
believe it would be worthwhile to include a short list in every lesson repo. 
This should/would be tailored to the audience of the lesson. I also think this 
list should be curated so that (as Darya suggested) it's content is a perfect 
fit for our learners ... if this is through a quick comment for every item or 
a 5-star rating, does not matter. But I think, it's important that we provide 
a quick statement how useful one title over another is. As a matter of fact, 
we as trainers/teachers are the ones that know the landscape of 
programming/scripting, our learners still need a map!

Also, I believe that the references on software-carpentry.org should stay. I 
consider useful overviews and some/most of them even stretch across topics 
(like the titles on open-source software development etc.) The global 
references page could then also link to the lessen references if needed.

Best -
Peter

On Wednesday, December 09, 2015 11:31:07 AM Darya Vanichkina wrote:
> Thanks for pointing that out, Peter! 
> 
> I think the way the literature is as a separate page gives a nice overview
> of the links we recommend (as opposed to embedded/scattered in/throughout
> the lessons). However, I do feel that page needs to be revamped, since it
> doesn’t seem to be very novice-friendly.
> 
> How clear would it be, for example, as a workshop attendee what I would
> learn by perusing " Effective Computation in Physics: Field Guide to
> Research with Python.” if what I’m told is  "Covers everything from basic
> shell scripting through object-oriented Python to parallel computing.”
> 
> OK, so basic shell scripting is important, but wait there was also this
> thing called the bash shell is this to do with it or am I building on it or
> using the python shell?….  Object oriented?… What does that mean? Is that
> good? Useful? Does this mean I’ll be able to do some fancy visualisation of
> my data and set up a website (which is what I really want)? Parallel
> computing? Why would I want to use parallel computing as a researcher? How
> does that even work?… … Should I even read this book if I’m not in physics?
> 
> Same with " Practical Computing for Biologists. “ - is it useful for non
> biologists? How?…
> 
> 
> What I am trying to say is that the list seems good in terms of content -
> although not exhaustive, and I’m sure we could add more favourite resources
> - but the descriptions are not very accessible to someone who doesn’t
> already know at least a bit of the lingo. 
> 
> Perhaps one way to address this might be to restructure the page more as a
> series of questions:
> 
> Did you love shell scripting? 
> If you’d like to learn more, Unix and Linux: Visual QuickStart Guide
> provides a very gentle introduction, and showcases how to do X, Y and Z
> (tasks that might be tempting to a researcher) 
> 
> 
> Would you like to harness the power of relational databases? 
> Chris Fehily's SQL describes the 5% of SQL that covers 95% of real-world
> needs. [And, yes, we also think that it moves a little slowly in some
> places, but the examples are really clear - for example, we really like the
> one where X, Y and Z are done (again, tempting real world use cases).
> 
> etc …
> 
> Thoughts?
> 
> Darya


___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

[Discuss] further reading

[Peter Steinbach]

Hi to all,

I was asked again recently, what books and/or websites I could recommend for 
learning to program in python. while thinking about the answer, I pondered the 
software carpentry website(s) and "only" found this:
http://software-carpentry.org/bib/reading.html
which is good to have and there potentially is more hidden on software-
carpentry.org.

I however wondered, if we could add a literature section to our lessons which 
would comprise curated resources both in terms of reading (i.e. books or 
weblinks) and websites for further self-paced learning. The web is full of 
material that could pick up our learners when they leave a boot camp. It 
doesn't have to be a long list, but at least something that some instructors 
could recommend or have tried and could say that it was a positive learning 
experience.

Before sending a PR, I wanted to have your opinion about it! Maybe something 
like this was left-out on purpose in the past?

Best,
Peter


___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

Re: [Discuss] pulling along those behind

[Peter Steinbach]

For all those interested, I finished a first version of the blog post on 
the etherpad. Feel free to dial over and provide feedback or make 
additions. I'd then convert this to a PR to the SWC site repo.


Best,
Peter

On 10/28/2015 09:59 AM, Greg Wilson wrote:

Hi everyone,

The simplest way to start might be to throw stuff into this Etherpad:
http://pad.software-carpentry.org/pulling-along-those-behind

Cheers,
Greg

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org



--
Peter Steinbach, Dr. rer. nat.
HPC Developer, Scientific Computing Facility

Scionics Computer Innovation GmbH
Löscherstr. 16
01309 Dresden
Germany

phone +49 351 210 2882
fax   +49 351 202 707 04
www.scionics.de

Sitz der Gesellschaft: Dresden (Main office)
Amtsgericht - Registergericht: Dresden HRB 20337 (Commercial Registry)
Ust-IdNr.: DE813263791 (VAT ID Number)
Geschäftsführer: John Duperon, Jeff Oegema (Managing Directors)

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

[Discuss] pulling along those behind

[Peter Steinbach]

Hi to all,

I just taught a SWC workshop for intermediates. As usual, a considerable 
portion of the audience would have been better off attending a novice 
course first. This time the ratio was quite high though: 30-40% out of 
25 IIRC.


My question is simple, how do other instructors deal with this 
situation? We had 2-3 helpers that jumped in and stood at the side of 
those completely lost. But me, the instructor, I need to adapt 
accordingly ... I simply took many detours and tried to explain more 
what I was doing ... which might have lead to more confusion than it 
should have.


What method do you guys use here?

Best,
Peter

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

Re: [Discuss] pulling along those behind

[Peter Steinbach]

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 feeling during the workshop that 
this pre-assessment only covered the tip of the iceberg (as expected).


I guess the trade-off who to bore and whom to carry through is always on 
the plate of the instructor. I'd have to say that being in a team of 2 
helps at this point tremendously as the co-instructor is among the 
"students" and simply can assist here and there.


If people have more feedback on the matter, I am happy to hear it. If 
not, my gratitude to those that replied already.


Best,
Peter

On 10/27/2015 03:27 PM, April Wright wrote:

Hi Peter-

I've been in this exact same situation, though with a departmental
workshop, rather than an SWC one. It's hard, and I'm sorry that happened to
you.

Since you're SWC, I think the first thing to do is ask the host. Often, the
host has some specific ideas about what they want the learners to come away
with, and that can help you steer the course.

What I did, in practice, was this: I spent way too much time helping
novices. I slowed down, got through less than half of the material, and the
intermediates, who had actually chosen the correct class and paid a nominal
fee for it were very unsatisfied. I really think that I made the wrong call
by punishing people who carefully read the sign-up and prioritizing those
who didn't. There are a lot of resources out there to help people take the
first steps in programming. There are fewer to help with the 'what's next',
and I should have been more sensitive to that fact. What I should have done
is told people who were working on novice-level skills that they were
welcome to stay and work, but that people working on the course material
would be assisted first.

On the next go around, I added a list of skills the learners needed to be
comfortable with to attend (previously, it had simply been a link to the
previous workshop) and a code snippet one of the students had written. I
let them know that this was the level of familiarity they needed to have *with
Python* to attend, and that TAs would preferentially assist those who were
mastering course skills over those who were mastering other material.

That worked, I only had one person for whom the course was inappropriate
(they were too high level) show up.

--a

-
Postdoctoral Researcher
Iowa State University, EEOB
University of Kansas, EEB
251 Bessey Hall
Ames, IA 50011
512.940.5761
http://wrightaprilm.github.io/
<http://wrightaprilm.github.io/pages/about_me.html>


On Tue, Oct 27, 2015 at 8:23 AM, Michael J Jackson <micha...@epcc.ed.ac.uk>
wrote:


Hi Peter,

If there are more people falling behind than you have helpers to handle,
then I'd just slow down. I'd (reluctantly) rather bore those who don't want
a slower pace, than confuse those do.

cheers,
mike


Quoting Peter Steinbach <steinb...@scionics.de> on Tue, 27 Oct 2015
11:39:01 +0100:

Hi Raniere et al,


thanks for the pointers for recording the terminal history, I'd like to
get back to my more general question though ... how to give participants
that are not up to the level of the course a chance to follow? I don't
wanna drag them all through, at some point there has to be a limit for the
sake of the remaining crowd. But still, I'd like to hear people's
experience on this.

Best,
Peter

On 10/27/2015 11:23 AM, Raniere Silva wrote:


Hi Peter,

Could you share these scripts?




Please check

https://github.com/swcarpentry/site/pull/1124/files#diff-9e17f2fd404c84648654a4fc54a9a2ecR71
.
We are going to publish it this week.

I'd like to see if they'd capture a nano screen etc

(I presume not, but I'd like to try them anyhow).
Apologies if they were already shared with this community and I
overlooked them.



There are terminal screen recorder that can capture nano
but from my experience they don't work for what you want. =(

Cheers,
Raniere



--
Peter Steinbach, Dr. rer. nat.
HPC Developer, Scientific Computing Facility

Scionics Computer Innovation GmbH
Löscherstr. 16
01309 Dresden
Germany

phone +49 351 210 2882
fax   +49 351 202 707 04
www.scionics.de

Sitz der Gesellschaft: Dresden (Main office)
Amtsgericht - Registergericht: Dresden HRB 20337 (Commercial Registry)
Ust-IdNr.: DE813263791 (VAT ID Number)
Geschäftsführer: John Duperon, Jeff Oegema (Managing Directors)

___
Discuss mailing list
Discuss@lists.software-carpentry.org

http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org







Dr. Michael (Mike) Jackson m.jack...@epcc.ed.ac.uk
Software Architect Tel: +44 (0)131 650 5141
EPCC, The University of Edinburgh  http://www.epcc.ed.ac.uk
Software Sustainability Institute  http://www.software.ac.uk


--
The University 

Re: [Discuss] a new lesson on Make

[Peter Steinbach]

Just to add:
msys2 (full blown Unix tool box for Windows) comes with a package 
manager that makes installing SWC tooling like make, git, python etc a 
piece of cake.


https://msys2.github.io/

Best,
Peter

On 06/29/2015 10:01 AM, Michael J Jackson wrote:

Hi Damien,

Quoting Damien Irving d.irv...@student.unimelb.edu.au on Mon, 29 Jun
2015 16:19:36 +1000:


Great - I think I'll teach this lesson at a workshop next month:
http://damienirving.github.io/2015-07-13-amos/

Naive windows question (i.e. I don't have a windows machine to try this
on): Does Make come with Git Bash?


(1) has Make info for all platforms. For Windows...

Once you have installed Git Bash you can install Make by:

* Download make.exe from here (2)
* Place it in the bin directory where you installed Git Bash e.g.
C:\Program Files (x86)\Git\bin.
* To test: open a Git Bash window, type make, and press Enter.
* You should see the following message

```
make: *** No targets specified and no makefile found. Stop.

```
This means that Make was successfully installed. Otherwise, you'll see
this error message:

```
bash: make: command not found
```

cheers,
mike

(1) http://hpcarcher.github.io/2014-12-03-edinburgh/
(2) https://github.com/msysgit/msysgit/blob/master/bin/make.exe?raw=true







On Fri, Jun 19, 2015 at 4:01 AM, Greg Wilson 
gvwil...@software-carpentry.org wrote:


We now have a lesson on using Make that's actually human-readable
(unlike
the one I did for version 4).  See
http://software-carpentry.org/blog/2015/06/adding-a-lesson-on-make.html
for the post - many thanks to Mike Jackson and Steve Croucher for
putting
it together.  Additions, corrections, suggestions, and everything else
would be very welcome.
Cheers,
Greg

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


___
Discuss mailing list
Discuss@lists.software-carpentry.org

http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org









Dr. Michael (Mike) Jackson m.jack...@epcc.ed.ac.uk
Software Architect Tel: +44 (0)131 650 5141
EPCC, The University of Edinburgh  http://www.epcc.ed.ac.uk
Software Sustainability Institute  http://www.software.ac.uk




___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org

[Discuss] Any SWC Folks in and around San Jose (CA)?

[Peter Steinbach]

Hi -

I'll be at the GTC2015 at San Jose Convention Center in about a week 
from now (March 16th to 20th).
I was wondering if other SWC Instructors will be there as well to meet 
up and exchange experiences on teaching the material? As I'll be there 
the whole week, meeting somewhere close in the bay area is also fine 
with me.


Best,
Peter

--
Peter Steinbach, Dr. rer. nat.
HPC Developer, Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany


phone +49 351 210 2882
fax   +49 351 210 1689
www.mpi-cbg.de

___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org