[Discuss] JOB: Biostatistician at Mt Sinai in NYC

[Noam Ross]

Hi all,

Job posting for an R-programming focused biostatistician job at Mt. Sinai
in NYC that would be a good match for an SWC person:
https://careers.mountsinai.org/find-your-place/jobs/biostatistician-i-department-of-environmental-medicine-and-public-health-new-york-ny

The PI, Allan Just, is a great person and very into reproducible research
and training. His CV/contact info here:
http://icahn.mssm.edu/profiles/allan-just

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

Re: [Discuss] Testing for data analysis code

[Noam Ross]

To me (and mostly from an R perspective), the major difference between unit
testing in packages and testing in analyses is that for the latter one
tests objects, not functions.  That is, rather than testing that a function
gives you a expected output for given inputs,  you are checking that
objects (data sets, fit models, summaries) have the properties you expect
given your analysis assumptions.  Most documentation and tutorials on
testing I've seen focuses on functions.

Object-based testing is for data sets is the approach used in the
assertr/validate/pointblank packages (for data in R), or TDDA (for data in
Python). I don't know of solutions tooled specifically to non-data
components of analyses. These are tough because some of them, like model
fit tests, can be subjective. I also don't know a great framework for
separating tests from analysis scripts, as you need access to your objects
to run tests.

FWIW, for the upcoming rOpenSci unconf we have two potentially related
projects: testing blocks for R markdown documents (
https://github.com/ropensci/unconf17/issues/38), and maybe something more
general for saving and testing objects (
https://github.com/ropensci/unconf17/issues/5).

On Wed, May 10, 2017 at 12:35 PM Pariksheet Nanda <
pariksheet.na...@uconn.edu> wrote:

> Hi Naupaka,
>
> I can't speak for what would be most successful in a classroom, though.
> For my graduate research work with R, I follow the guidelines of
> http://r-pkgs.had.co.nz/ without changing much namely:
>
> 1) Create a package with devtools, then create the analysis script in
> vignettes/ with devtools::use_vignettes("name-of-vignette").  Edit the Rmd
> file and run code blocks with Ctrl+Enter.
> 2) Create functions as needed in the R/ directory.
> 3) Add dependencies directly to DESCRIPTION (one could also use use
> devtools::use_package())
> 4) Update NAMESPACE from Roxygen comments in R/ files with
> devtools::document()
> 5) Add testthat unit tests for those R functions.
> 6) Once in a while run devtools::check()
>
> The book introduction suggests that this practice is somewhat typical (
> http://r-pkgs.had.co.nz/intro.html) and am curious about others'
> experiences.
>
> There is some cognitive overhead of working with packages for newer
> programmers, so you may want to have the workflow and gotchas in a
> cheatsheet or require some amount of prior R experience for the students to
> value that particular way of doing things.
>
> Pariksheet
>
> ___
> 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] nano clean the window scrool in Windows (was Re: nano not found after installing gitbash (Raniere Silva))

[Noam Ross]

I support this, but I think the appropriate approach is to gather
evidence.  Many (most?) changes to lessons and methods start as experiments
by instructors, so I think a set of instructors should produce the
following for an upcoming workshop, which other instructors can try out:

-   A fork of the workshop webpage with install instructions
-   A fork of the shell lesson
-   A fork of the git lesson

Then, following some reports from instructors after a few workshops and a
few inevitable tweaks, we can see if this merits widespread adoption.

I agree with Tracy that command-line editor skills are potentially useful
for many learners, but I think (without real evidence) that (a) learning a
simple command line editor like nano is a low barrier *once one is familiar
with the shell and the notion of a text editor already*, so people using
remote machines will be much of the way there under this approach, and (b)
the overall gain in improved workshop flow may be more important.  A
command-line editor may be one of the things one "demos" in a workshop
where learners have a question or one anticipates that some have immediate
remote computing needs.

On Thu, Mar 30, 2017 at 5:58 AM Raniere Silva  wrote:

> Hi all,
>
> today at the workshop,
> one of the our Windows learners asked me why after quit nano the
> previous command weren't available when scroll the window up.
> The learner was very annoyed to not be able to see the history.
>
> I would like to motion to change nano with Atom as the recommended/default
> text editor for our workshops. I don't want to start yet another flame war,
> we already had lots and lots of discussion about this,
> so I will summarise the benefits and drawback of my proposal.
> I will ask that before suggest another text editor instead of Atom,
> stop and think that the text editor will benefit novice learners
> instead of just make your life easy as instructor because you use X on
> your daily work. (I don't use Atom!)
>
> # Benefits
>
> - Is open source.
> - (Just) works in Windows, Mac and Linux.
> - Easy to install in Windows, Mac and Linux.
> - "All versions" are available to Windows, Mac and Linux.
>
>   Some software, e.g. Skype, works in Windows, Mac and Linux but
>   different versions are available to different OS.
> - Configure PATH to be accessible from Git Bash.
>
>   No need for extra configuration or our script to fix PATH.
> - Well mantained and supported.
> - Syntax highlight out of the box (AFAIK).
> - Lots of plugins for learners that decide to keep using Atom.
>
>   AFAIK there is a plugin that allow learners to use Atom
>   to edit remote files, e.g. on clusters.
> - Beautiful interface.
>
> # Drawback
>
> - Learners and instructions will need to switch windows.
>
> # (My own) conclusions
>
> Replace nano with Atom will avoid many of the our issues during the
> workshop, such as "we will use nano but if you don't have nano you can
> use X", and reduce the volunteer work that we need to maintain the
> quality of our workshops. The price that we will need to pay is switch
> windows during the workshop.
>
> Thanks,
> Raniere
> ___
> 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] Qualitative data analysis - free tools?

[Noam Ross]

We had a tutorial on RQDA at our users group meeting at Davis a couple of
years ago. Slides and video:
http://www.noamross.net/blog/2015/5/28/johnson-rqda.html

On Wed, Mar 15, 2017, 3:28 AM Anelda van der Walt 
wrote:

> Dear community,
>
> We are looking for a free alternative to AtlasTI for qualitative data
> analysis.
>
> I've come across RQDA (http://rqda.r-forge.r-project.org/). The benefit
> of teaching RQDA to novices, as I see it, is that it gives us an
> opportunity to also expose them to R and all the other great things you can
> do with R (not only qualitative). Obviously this also aligns nicely with
> our new partnership with the Carpentries and the type of workshops we are
> already planning.
>
> I am not familiar with either AtlasTI or RQDA though and was wondering if
> anyone might have an opinion about RQDA and whether this might be a
> sensible way forward or if there is anything else that might be more
> suitable?
>
> I'd appreciate any inputs, pointers to tutorials, etc.
>
> Thanks as always!
>
> Kind regards,
>
> Anelda
> ___
> 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] RR dplyr lesson

[Noam Ross]

The gapminder data has class `tbl_df`, meaning it is treated as a "tibble",
but only if dplyr is loaded.  Tibble/dplyr subsetting works slightly
differently, in that it does not reduce a 1-column data frame to a vector
by default.:

```
library(gapminder)
a <- gapminder[gapminder$continent == "Africa", "gdpPercap"]
library(dplyr)
b <- gapminder[gapminder$continent == "Africa", "gdpPercap"]
str(a)
#>  num [1:624] 2449 3014 2551 3247 4183 ...
str(b)
#> Classes 'tbl_df', 'tbl' and 'data.frame':624 obs. of  1 variable:
#>  $ gdpPercap: num  2449 3014 2551 3247 4183 ...
mean(a)
#> [1] 2193.755
mean(b)
#> Warning in mean.default(b): argument is not numeric or logical: returning
#> NA
#> [1] NA
```



On Wed, Feb 15, 2017 at 10:41 AM Christopher Hamm 
wrote:

> Hello all,
>
> While preparing for a workshop I was running through the code for the
> Reproducible Research with R lessons and I found an odd behavior that I
> have not encountered before in the [dplyr tutorial](
> https://swcarpentry.github.io/r-novice-gapminder/13-dplyr/).
>
> If I load load ‘gapminder' and ‘dplyr' and then run the first line of code:
>
> `mean(gapminder[gapminder$continent == "Africa", "gdpPercap"])`
>
> Returns:
>
> `[1] NA
> Warning message:
> In mean.default(gapminder[gapminder$continent == "Africa", "gdpPercap"]) :
>   argument is not numeric or logical: returning NA`
>
> If I only load ‘gapminder' the code works properly. I’ve replicated this
> on four different machines and am scratching my head as to why this error
> occurs when I load ‘dplyr’. Any thoughts?
>
> Chris Hamm
>
> ___
> 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] Standard USB install setup/image

[Noam Ross]

I was wondering if anyone had documented or standardized a typical setup
for creating USB install drives for workshops with poor wifi.

For R workshops, I believe I would use miniCRAN to create a local
repository for all the packages required, in addition to the R/RStudio/git
binary installers.

I'm not sure what the equivalent would be for Python, and I want to make
sure I don't miss anything required for all operating systems.
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/listinfo/discuss

Re: [Discuss] using GitHub for paper submission and review

[Noam Ross]

We've been running rOpenSc package submissions in a similar way for a
couple of years and JOSS's process is derived from ours.  The main
difference is (1) reviews are not anonymous, but public, so no temporary
accounts are created or needed, and (2) in our case the author's repo is
merged in after acceptance, in JOSS's case the repo is never merged in, but
the paper (a markdown file), is extracted from the repo and compiled by a
bot.

I think the workflow you describe could be enabled by a bot similar to
JOSS's *wheedon* bot, which could extract a paper, submit it to a
*private* repository
and start a review chain.  I'm not sure how to enable anonymous accounts.
If every paper was a private repository within an organization, then you
could limit access to just the reviewers, and then extract the content to
show the author. This wouldn't allow them to respond in the thread, though.

On Tue, Oct 18, 2016 at 6:04 PM Damien Irving 
wrote:

> Hi Greg,
>
> I'm pretty sure that the Journal of Open Source Software runs its entire
> review process through GitHub. (Although I'm not sure how many of your dot
> points their process covers.)
> http://joss.theoj.org/
>
> There are a number of Software Carpentry people involved with that journal.
>
>
> Cheers,
> Damien
>
> On Wed, Oct 19, 2016 at 8:20 AM, Greg Wilson <
> gvwil...@software-carpentry.org> wrote:
>
> Hi,
>
> I was speaking with a colleague last week about the possibility of using
> GitHub to manage paper submissions and reviews.  The journal in question
> doesn't do open/accredited reviews, so I was wondering if anyone had any
> experience with the following workflow:
>
> - author submits paper by sending URL of public GitHub repo to journal
>
> - journal creates private repo and merges author's submission into
>
> - journal creates temporary accounts with auto-generated names for
> reviewers and gives them access to the newly-created private repo
>
> - reviewers post comments: authors and editors can see them/respond to
> them, but identities of reviewers are known only to editors
>
> - authors make changes in the private repo in response to reviewers'
> comments, and merge from that to their public repo when they want to
>
> Thanks,
>
> Greg
>
> --
> Dr Greg Wilson
> Director of Instructor Training
> Software Carpentry Foundation
>
> ___
> 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] Excel errors.... (Tiffany Timbers)

[Noam Ross]

I have recently tried using airtable.com for a couple of projects. With it,
you can create databases of linked tables, enter data in a spreadsheet-like
or form mode with constrained data types (including image/file uploads),
and access everything via CSV download or REST API (for which there is an R
wrapper). It has a nice mobile app for field data entry if the form is not
very complicated. I like it a lot, though it is new, its versioning system
is sort of weird, and it is online-only.

On Fri, Aug 26, 2016, 6:19 PM Gabriel A. Devenyi  wrote:

> LibreOffice also has a database tool
> https://www.libreoffice.org/discover/base/
>
> On Fri, Aug 26, 2016, 18:16 Tiffany Timbers 
> wrote:
>
>> Emily Jane asked a good question about what are the other options, aside
>> from Excel, Libre Office, or text editors as a means for data entry.
>>
>> Forms, whose output can later be accessed as tabular data (e.g., CSV),
>> are a solution I have used and liked. Proprietary database software, such
>> as Filemaker Pro exists, and from my experience, is fairly user friendly.
>> For open source options, I would use Google forms, or if you want an option
>> that doesn’t have to be hosted on the web, you could try out Dean Attali’s
>> shinyforms R package (works, but is still under development) [1].
>>
>> I especially like forms for data entry, as you can more easily constrain
>> how the data gets entered (predefined columns, drop-down menus with limited
>> options, etc), compared to the free-for-all that exists with a spreadsheet.
>>
>> I’d love to hear other’s favourite tools and opinions on this topic.
>>
>> Cheers,
>> Tiffany
>>
>> [1] https://github.com/daattali/shinyforms
>>
>> Tiffany Timbers
>> tiffany.timb...@gmail.com
>>
>>
>>
>>
>> --
>>
>> Message: 4
>> Date: Fri, 26 Aug 2016 15:02:06 -0700
>> From: Emily Jane McTavish 
>> To: Software Carpentry Discussion
>> 
>> Subject: Re: [Discuss] Excel errors
>> Message-ID: <80cea324-0514-6871-0f3d-42bb5bc1b...@gmail.com>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Great points.
>>
>> I have a question about alternatives to excel for data input.
>>
>> Following this paper I have seen a lot of 'never use Excel' tweets, but
>> that seems to be ignoring a key step in real world data analysis
>> pipelines. If data is not coming straight off a machine, such as in
>> ecological surveys, behavioral experiments, meta-analyses of gene names,
>> etc., those data need to be put into a tabular, machine readable, format
>> (e.g. CSV) somehow. I don't think anyone is recommending using a text
>> editor to do that.
>> Libre office calc and google sheets have many of the same autoformat
>> issues as Excel. (although that may be fixed in new versions of libre
>> office?)
>>
>> I think when people say 'don't use excel', they often mean 'for
>> analysis', or 'for statistics'. But this paper demonstrates it is
>> problematic for even simple data input. I know what to recommend as
>> alternatives in the former cases, but not for the latter. Am I missing
>> good alternative options here?
>>
>>
>> Thanks,
>> Emily Jane
>>
>> --
>> Emily Jane McTavish
>> Assistant Professor
>> School of Natural Sciences
>> University of California, Merced
>> 5200 N. Lake Rd, Merced CA 95343
>> ejmctav...@gmail.com, ejmctav...@ucmerced.edu
>>
>>
>>
>>
>> On 08/26/2016 02:42 PM, Steven Haddock wrote:
>>
>> I was going to post that article too, but I dug into it (read the paper),
>> and it is really just conversion of gene names (like SEPT5) in
>> supplementary files. That was reported long ago as affecting some
>> quantifications, but I would call it analytical errors as we have seen in
>> the past. A bit of a tempest in a teapot, perhaps.
>>
>> Ironic twist, the paper provides a supplementary file listing all the
>> gene-name errors they found, posted as an Excel file.
>>
>> -Steve
>>
>> On Aug 26, 2016, at 14:26 , Maxime Boissonneault <
>> maxime.boissonnea...@calculquebec.ca> wrote:
>>
>> Hi everyone,
>> Some interesting content to use about how to not do science correctly
>> with a computer
>>
>> https://www.washingtonpost.com/news/wonk/wp/2016/08/26/an-alarming-number-of-scientific-papers-contain-excel-errors/
>>
>>
>> Maxime Boissonneault
>> ___
>> 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
>>
>>
>>
>>
>> --
>>
>> Subject: Digest Footer
>>
>> ___
>> Discuss mailing list
>> Discuss@lists.software-carpentry.org
>> http://lists.software-carpentry.org/listinfo/discuss
>>
>> 

[Discuss] Job: Postdoctoral Fellow in Infectious Disease Data Science

[Noam Ross]

Hi all,

We're hiring a postdoc at my organization, and someone with SWC skills and
some knowledge of infectious disease would likely fit the bill.  Info at
http://www.ecohealthalliance.org/careers#pg-102-1 and pasted below.   Feel
free to get in touch with me about more details.

Noam

---

Postdoctoral Fellow

April 1, 2016
EcoHealth Alliance is seeking a Postdoctoral Fellow for the Data &
Technology Team. As part of a small team of engineers, data scientists, and
infectious disease scientists, you’ll develop tools to support EcoHealth
Alliance’s mission in conservation and global public health. The focus of
this position will be to develop global health web platforms that are
actively used to monitor global emerging infectious diseases, and that
contribute to the analysis of disease emergence.

DESCRIPTION AND RESPONSIBILITIES

We are looking to build a diverse team with a variety of skill sets and
backgrounds. Position duties may include:

Research - Collect and analyze primary and secondary data in infectious
disease modeling, forecasting, and policy analysis research. Using applied
modeling on the contribution of infectious diseases to the state and region
and applied policy systems analysis, scenario development, and criteria
analysis.
Data Management and Project Supervision - Responsible for the storage,
organization, and security data using qualitative and quantitative
procedures. The fellow will coordinate and supervise undergraduate and
graduate level student assistants working on related projects, including
establishing collection, analysis, and storage management protocols, and
data quality monitoring.
Presentation of Research Results - Coordinate with collaborating authors on
revisions, analysis, and presentation of findings; use findings from public
health and infectious disease modeling to prepare manuscripts intended for
professional publication in peer-reviewed journals; maintain professional
relationships with key stakeholders, agency, and industry representatives
to obtain sensitive information, convey results of analysis, and seek
feedback on key operational and research questions; prepare and deliver
presentations at professional meetings.

QUALIFICATIONS

Minimum Qualifications

Completed Ph.D. in Public Health, Environmental Health, Epidemiology,
Biostatistics, Infectious Disease Ecology, Data Science or related field at
the time of starting the position
Experience competing for external funding
Experience publishing research in refereed journals relevant to the field
of study
Experience in working across diverse disciplines
Strong analytical or modeling skills in applied public health and
infectious diseases
Strong verbal and written communication skills
Preferred Qualifications

At least two years educational and work experience related to infectious
diseases
Strong data management and project management skills
Experience in statistical analysis, data management, and interpretation of
data
Demonstrated ability to learn advanced modeling techniques with an interest
in infectious disease forecasting, big data, and data visualization
EcoHealth Alliance is an equal opportunity employer offering competitive
salary and a comprehensive benefits package that covers 100% of the monthly
health care premium costs for the employee and their family when applicable
(including dental and vision coverage), a 403(b) pension plan, flexible
work schedules, a minimum of 10 days paid vacation annually, paid holidays,
work from home days, and pre-tax transportation withholding for commuters
in New York City. EcoHealth Alliance may encourage employees to attend
conferences when appropriate, and enroll in courses for the joint purposes
of professional development and promoting the EcHealth Alliance mission.
The position is based at EcoHealth Alliance’s headquarters in New York City
(Manhattan). Local candidates are preferred with possible relocation
assistance available. Outstanding remote candidates will also be
considered, but must be available to work for at least 4 hours between 9am
and 6pm Eastern Standard Time to facilitate collaboration with New York
based employees.

HOW TO APPLY:

To apply, you must send your resume and a personalized cover letter as one
document to h...@ecohealthalliance.org with the subject of “Postdoctoral
Fellow 2016". Applications without cover letters will not be evaluated.
This cover letter will help us assess your ability to communicate
effectively and will be used as the primary mechanism to determine whether
a candidate is asked to interview for the vacant position. The cover letter
is the most important part of your application. In your cover letter,
please briefly describe your background and any experience you may have
with web development frameworks, machine learning, natural language
processing and public health. Be sure to mention why you are interested in
working on a research-and-development oriented team at a health and
conservation focused non-profit.

THANK 

[Discuss] Teaching git via other UIs (was: from reproducibility to over-reproducibility)

[Noam Ross]

I learned to use git via the RStudio GUI. It is not the most powerful
interface, but it was enough for most tasks I needed as a beginner:
committing, reviewing history, pushing/pulling from Github, etc. As I
became comfortable with the concepts and had more advanced needs I switched
to the command line.

For R-based SWC/DC workshops I have taught and seen, we often teach git in
the command line and then afterwards briefly demo the fact that similar
tasks can be accomplished in the RStudio IDE, which learners already have
installed. Has anyone attempted to teach with the GUI first, or somehow
teach them in parallel? I hypothesize learners might be more likely to use
git immediately with this approach.

Two other thoughts on this approach:

1. While we aim to teach script-ability, scripting git commands is
rare/advanced use.
2. I have gotten feedback that teaching the RStudio git GUI is hard to
follow.  This seemed to be because (1) this was a less well-developed
lesson - more a demo at the end of the main git lesson, and (2) learners
could not follow along via SWC notes or the live command history we shared
via dropbox.  So such lesson might require a screenshot-heavy set of
accompanying lesson notes.  Guidance might come from the DC experience with
OpenRefine and Excel lessons.

- Noam

On Wed, Mar 2, 2016, 7:54 AM Konrad Hinsen 
wrote:

> On 02/03/16 10:30, Juan Nunez-Iglesias wrote:
>
> > I hope we all migrate soon to UIs built on top of git, such as gitless
> > . But it's gonna be slow and painful, because of
> > the huge momentum that git has.
>
> I considered using gitless instead of git for my recent course for
> French PhD students
> (https://github.com/khinsen/FdV-Computer-Aided-Research-2016). The two
> main reasons I ended up sticking to plain git were
>
> 1) Gitless requires additional installation, whereas plain git was
> already available on all machines.
>
> 2) There is excellent SWC teaching material for Git, but not for gitless.
>
> So, yes, SWC is becoming a part of the "system inertia" for me!
>
> A problem I see with gitless is that it is technically compatible with
> git, but not operationally. For a given local repository, you use either
> git or gitless. For everyone who knows some git commands, that means
> unlearning.
>
> What I use myself is Magit (http://magit.vc/) within Emacs. It's a much
> more reasonable UI for git, but it's fully compatible with git (it
> actually calls git under the hood), so you can mix it with command line
> work. But I wouldn't consider Magit for teaching because I am not
> looking forward to doing "introduction to Emacs" first!
>
> Konrad.
>
>
>
> ___
> 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] installation instructions

[Noam Ross]

It would make sense for each lesson to have a link to the install lesson,
though.

On Wed, Feb 17, 2016 at 7:35 PM Matt Davis  wrote:

> The idea of an installation lesson sounds good to me.
>
> On Wed, Feb 17, 2016 at 4:28 PM Darya Vanichkina 
> wrote:
>
>> A separate install lesson, because the lessons are already rather
>> content-heavy, and searching within them for install instructions to email
>> to students to have a go before coming in is confusing.
>>
>>
>> On 18 February 2016 at 11:16:34, Moreau, John (UMKC-Student) (
>> john.r.mor...@mail.umkc.edu) wrote:
>> > Matt et al:
>> > Perhaps this is the crux of the problem. We no longer have installation
>> instructions
>> > outside of the workshop pages. More experienced instructors may know to
>> check the workshop
>> > template on GitHub. However, for newer instructors, potential workshop
>> hosts, and
>> > drive-by site visitors, there’s no clear directions.
>> > Thinking about the problem from the perspective of a novice learner,
>> their first instinct
>> > will be to check the website. After coming up short, some people will
>> become frustrated
>> > and abandon the search. Here’s where an expert might say “Why didn’t
>> you just* google
>> > for {program needed}?” Because the novice learner lacks the mental
>> models of an expert,
>> > they may not know what search terms to use. The Shell lessons suffer
>> from this problem
>> > more than most:
>> >
>> > · Nowhere on the lesson landing page (
>> http://swcarpentry.github.io/shell-novice/)
>> > do we mention the term “Bash”
>> >
>> > · The “Introducing the Shell” page (
>> http://swcarpentry.github.io/shell-novice/00-intro.html)
>> > does not use the term “Bash” until the seventh paragraph
>> >
>> > · The intro page does not directly tell a novice learner that the
>> standard Git for Windows
>> > installation includes Bash.
>> >
>> > · The intro page does mention that the Bash shell is the default shell
>> on many modern UNIX
>> > implementations. A novice learner may not know that Mac OS now uses a
>> UNIX engine and uses
>> > Bash for its command line terminal. They also may not know how to
>> access the terminal.
>> >
>> > · If a Linux user doesn’t know about the Unix command line, I really
>> want to ask them how
>> > they got Linux on their machine in the first place.
>> >
>> > For these reasons, I suggest that we should add installation
>> instructions to either
>> > the lesson pages or as a separate “lesson”. Before Greg (or anyone
>> else) says it, yes,
>> > I know “Pull requests are always welcome”. Let me ask the community -
>> Would you rather
>> > have:
>> > A separate install “lesson” and links from the other lessons to that
>> install page
>> > -OR-
>> > Installation information within each separate lesson?
>> >
>> > John Moreau
>> > * http://swcarpentry.github.io/instructor-training/05-expertise.html
>> >
>> > From: Discuss [mailto:discuss-boun...@lists.software-carpentry.org] On
>> Behalf
>> > Of Matt Davis
>> > Sent: Wednesday, February 17, 2016 5:05 PM
>> > To: Markus Mueller ; discuss@lists.software-carpentry.org
>> > Subject: Re: [Discuss] installation instructions
>> >
>> > Hi Markus,
>> >
>> > Our workshop webpages have software installation instructions. We used
>> to have those
>> > on software-carpentry.org, but I couldn't find
>> > them so here's the website of an upcoming workshop:
>> https://joshwaterfall.github.io/2016-02-16-NIH/
>> >
>> > Best,
>> > Matt
>> >
>> > On Wed, Feb 17, 2016 at 2:53 PM Markus Mueller >
>> > wrote:
>> > Dear listers,
>> >
>> > I am a new instructor (or soon to be one) and started having a closer
>> look at the software
>> > carpentry lesson material. I first had a look at the instructor guide (
>> http://swcarpentry.github.io/shell-novice/instructors.html)
>> > and only found some general tips and hints about which tools to use and
>> how to install them
>> > (my interested would here apparently be how to get a unix shell to run
>> on windows).
>> >
>> > I apologize if I missed something, but otherwise would be glad if
>> somebody could point
>> > me to the installation guidelines (that the page above somehow hints
>> at).
>> >
>> >
>> > Cheers,
>> >
>> > Markus
>> >
>> > 
>> >
>> > Please consider the environment before printing this email
>> > Warning: This electronic message together with any attachments is
>> confidential. If
>> > you receive it in error: (i) you must not read, use, disclose, copy or
>> retain it; (ii) please
>> > contact the sender immediately by reply email and then delete the
>> emails.
>> > The views expressed in this email may not be those of Landcare Research
>> New Zealand Limited.
>> > http://www.landcareresearch.co.nz
>> > ___
>> > 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

[Noam Ross]

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 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 

Re: [Discuss] Asking multiple choice questions during a workshop

[Noam Ross]

Discourse has a quick and easy markdown-based poll feature:
http://try.discourse.org/t/poll-do-you-have-polls/172

Of course, you need a discourse forum running to use this, but you could
add as many polls as you want in a forum thread, and the forum might be
useful in other ways.
On Fri, Sep 4, 2015 at 7:46 AM Maxime Boissonneault <
maxime.boissonnea...@calculquebec.ca> wrote:

> It does not. At least according to the video, you can do "quick question",
> which you enter on the fly.
>
>
> Le 2015-09-04 10:45, Lex Nederbragt a écrit :
>
> I have seen it in action, but it requires me to enter the questions I want
> to ask beforehand - or ask blank questions as I already do with the google
> form...
>
> Alternatives are kahoot.it (more playful) and mentimeter ($, I have
> access through my university).
>
> Lex
>
>
> On 04 Sep 2015, at 16:40, Maxime Boissonneault <
> maxime.boissonnea...@calculquebec.ca> wrote:
>
> Hi Lex,
> Have you given Socrative.com a shot ?
>
> Maxime Boissonneault
>
> Le 2015-09-04 10:37, Lex Nederbragt a écrit :
>
> Hi,
>
> As I wrote elsewhere
> 
>  (thanks
> to Greg for mentioning this post on the SWC blog), for collecting answers
> to the multiple choice questions I ask during the workshops I teach, I use
> a very simple google form with no question-text, and four answers: ‘option
> 1, option 2, option 3, option 4’. The ‘summary of responses’ option from
> google allows me to show students the tally of responses. For the second
> round of voting, and for each next question, I simply delete all responses.
>
> The reason I am doing this is that it saves me from having to enter all
> possible questions in forms, and gives me the flexibility to decide on the
> spot which question from the available set I ask (in one case I had
> prepared a slide for each question in the unix lesson, in another I simply
> used the projector to show the question from the SWC unix lesson page in
> the browser). This works very well as an instructor and is easy enough to
> do. One tip: don’t show the tally before everyone has answered (use a
> separate laptop/tablet for yourself, or freeze the projectorscreen while
> you check the responses).
>
> One drawback is that I loose all votes for future reference (ie. figuring
> out which question was too say or too hard)[1].
>
> I can’t help thinking, though, that in 2015 we should be able to do this
> in a better way. I have for a long time hoped for a markdown-based
> questionnaire system: write questions in markdown, and render these into an
> online form for collecting answers, coupled with a way to retrieve all
> answers in text files. This would make it much easier to reorganise/reuse
> questions, and would allow version control/diff/pull requests. Does anyone
> know whether there is such a software?
>
> If not, could this be an SWC-inspired coding project? We would really be
> helped by a system that pulls the questions from the instructor’s clone of
> the lesson material repo and auto-generates forms for each workshop. Maybe
> a long shot, but I though it worth asking.
>
> Lex
>
> [1] Well, in fact, even after resetting the responses, you can still see
> all answers in the underlying google spreadsheet, and use the timestamps to
> reverse engineer which question you asked for which set of ansers. Or take
> screenshots along the way. Still, rather impractical...
>
>
>
> ___
> Discuss mailing 
> listDiscuss@lists.software-carpentry.orghttp://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org
>
>
>
> --
> -
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Instructeur Software Carpentry
> Président - Comité de coordination du soutien à la recherche de Calcul Québec
> Ph. D. en physique
>
>
>
>
> --
> -
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Instructeur Software Carpentry
> Président - Comité de coordination du soutien à la recherche de Calcul Québec
> Ph. D. en physique
>
> ___
> 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] Asking multiple choice questions during a workshop

[Noam Ross]

Not as far as I can tell
On Fri, Sep 4, 2015 at 8:02 AM Lex Nederbragt <lex.nederbr...@ibv.uio.no>
wrote:

>
>
> On 4 Sep 2015, at 16:55, Noam Ross <noam.r...@gmail.com> wrote:
>
> Discourse has a quick and easy markdown-based poll feature:
> http://try.discourse.org/t/poll-do-you-have-polls/172
>
> Of course, you need a discourse forum running to use this, but you could
> add as many polls as you want in a forum thread, and the forum might be
> useful in other ways.
>
>
> Hmm... Can you disable viewing of responses while people answer?
>
>Lex
>
> On Fri, Sep 4, 2015 at 7:46 AM Maxime Boissonneault <
> maxime.boissonnea...@calculquebec.ca> wrote:
>
>> It does not. At least according to the video, you can do "quick
>> question", which you enter on the fly.
>>
>>
>> Le 2015-09-04 10:45, Lex Nederbragt a écrit :
>>
>> I have seen it in action, but it requires me to enter the questions I
>> want to ask beforehand - or ask blank questions as I already do with the
>> google form...
>>
>> Alternatives are kahoot.it (more playful) and mentimeter ($, I have
>> access through my university).
>>
>> Lex
>>
>>
>> On 04 Sep 2015, at 16:40, Maxime Boissonneault <
>> maxime.boissonnea...@calculquebec.ca> wrote:
>>
>> Hi Lex,
>> Have you given Socrative.com a shot ?
>>
>> Maxime Boissonneault
>>
>> Le 2015-09-04 10:37, Lex Nederbragt a écrit :
>>
>> Hi,
>>
>> As I wrote elsewhere
>> <https://flxlexblog.wordpress.com/2015/08/31/active-learning-strategies-for-bioinformatics-teaching-2/>
>>  (thanks
>> to Greg for mentioning this post on the SWC blog), for collecting answers
>> to the multiple choice questions I ask during the workshops I teach, I use
>> a very simple google form with no question-text, and four answers: ‘option
>> 1, option 2, option 3, option 4’. The ‘summary of responses’ option from
>> google allows me to show students the tally of responses. For the second
>> round of voting, and for each next question, I simply delete all responses.
>>
>> The reason I am doing this is that it saves me from having to enter all
>> possible questions in forms, and gives me the flexibility to decide on the
>> spot which question from the available set I ask (in one case I had
>> prepared a slide for each question in the unix lesson, in another I simply
>> used the projector to show the question from the SWC unix lesson page in
>> the browser). This works very well as an instructor and is easy enough to
>> do. One tip: don’t show the tally before everyone has answered (use a
>> separate laptop/tablet for yourself, or freeze the projectorscreen while
>> you check the responses).
>>
>> One drawback is that I loose all votes for future reference (ie. figuring
>> out which question was too say or too hard)[1].
>>
>> I can’t help thinking, though, that in 2015 we should be able to do this
>> in a better way. I have for a long time hoped for a markdown-based
>> questionnaire system: write questions in markdown, and render these into an
>> online form for collecting answers, coupled with a way to retrieve all
>> answers in text files. This would make it much easier to reorganise/reuse
>> questions, and would allow version control/diff/pull requests. Does anyone
>> know whether there is such a software?
>>
>> If not, could this be an SWC-inspired coding project? We would really be
>> helped by a system that pulls the questions from the instructor’s clone of
>> the lesson material repo and auto-generates forms for each workshop. Maybe
>> a long shot, but I though it worth asking.
>>
>> Lex
>>
>> [1] Well, in fact, even after resetting the responses, you can still see
>> all answers in the underlying google spreadsheet, and use the timestamps to
>> reverse engineer which question you asked for which set of ansers. Or take
>> screenshots along the way. Still, rather impractical...
>>
>>
>>
>> ___
>> Discuss mailing 
>> listDiscuss@lists.software-carpentry.orghttp://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org
>>
>>
>>
>> --
>> -
>> Maxime Boissonneault
>> Analyste de calcul - Calcul Québec, Université Laval
>> Instructeur Software Carpentry
>> Président - Comité de coordination du soutien à la recherche de Calcul Québec
>> Ph. D. en physique
>>
>>
>>
>>
>> --
>> -
>> Maxime Boissonneault
>> Analyste de calcul - Calcul Québec, Université Laval
>> Instructeur Software Carpentry
>> Président - Comité de coordination du soutien à la recherche de Calcul Québec
>> Ph. D. en physique
>>
>> ___
>> 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

[Discuss] Examples of beginner problems

[Noam Ross]

I've been trying to figure out a good way to teach a getting unstuck
lesson that would include:

-   Navigating and searching help files
-   Googling problems and error messages, and good web resources
-   Debugging code
-   Help fora and writing minimum reproducible examples (MREs)

One of the biggest challenges thinking about this has been finding problems
that could be presented as examples or exercises. So I went through the
archives of our local R support listserv and pulled out some actual posts
and put them a repo:
https://github.com/noamross/zero-dependency-problems-r/tree/master

These are all in R and are zero dependency, in that they are about base R
problems rather than package-specific ones [^1].  In general they are short
and require not much more knowledge (though perhaps more expertise) than
taught in an SWC workshop.  Only some are MREs, but I like this because
they help think about how to make MREs.

I hope people can contribute more examples, including python/shell/(git?).
I think wild caught questions are a good starting point, though it may
make sense to modify them for teaching purposes.  It would probably make
sense to categorize these once there are enough.

Thoughts? Please respond in the repo issues.

Noam

[^1]: Although I note the vast majority of questions I slogged through ARE
about package-specific issues, which makes me think that it's important to
teach about packages and package ecosystems.
___
Discuss mailing list
Discuss@lists.software-carpentry.org
http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org