[REVIEW]: Quantitative Big Imaging about jose-reviews HOT 31 CLOSED

I've updated the URL of the repository address to https://github.com/kmader/Quantitative-Big-Imaging-2018 which has fixed this.

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👋 @kmader Happy New Year!
How are the revisions coming along? Give us a quick update, when you can. Thanks!

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @arokem, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

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Attempting PDF compilation. Reticulating splines etc...

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PDF failed to compile for issue #25 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
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from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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PDF failed to compile for issue #25 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in collect!'
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Hmm… did you change anything from the Pre-Review stage, @kmader ?

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@labarba Not that I know of, I don't immediately see what the error message is, is something I can change or try?

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I think the message means that the paper file is not being found. @arfon ?

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It's because this URL doesn't resolve:

https://github.com/kmader/Quantitative-Big-Imaging-2018/tree/jose-submission

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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--> Check article proof 📄 <--

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This submission includes a set of materials that were created for the teaching of an image processing course at the ETH in Spring 2016. The course includes lectures about a large range of topics in image processing, introducing modern methods in computational science along the way. From what I could gather from watching the lecture videos and going through the materials, it looks like the course was fantastic. I wish that these topics would have been taught to me early on in this way.

As I said, the materials provided in the repository, including lecture videos, notebooks, and slide-decks are excellent, and could potentially be made very useful as a set of reusable materials that others could pick and choose from, when designing courses, or even as materials for self-teaching. However, as the submission is currently organized, it carries with it too much of the legacy of its original provenance as it was written to accompany a particular course in a particular time and place. I think that for this to be a valuable contribution in this context, and to facilitate reusability, some of this specific context might need to be set aside, in favor of a more general set of materials, targetted at reuse.

For example, I think that many of the slide-decks are not currently useful to anyone who wasn't in the class, without additional notes that would tell us what to do with these slides. For example, the slides for the second lecture are useful as an accompaniment to the lecture that Dr. Kaestner gave, but are not necessarily useful to anyone without detailed notes from that lecture. A similar issue arises with Dr. Prummer's slides (from May 17th), but even worse, because no video is provided for this lecture. Similar can be said for many other lecture materials, that do not stand on their own, and I believe cannot currently be effectively reused, without substantial additional effort.

An overall guide in the readme that tells potential users of these materials (learners and instructors) how they should use the materials would be useful. Detailed narrative notes to accompany the lectures or at least more notes in the slides and notebooks would help.

The profusion of materials and lack of guidance on how to proceed through the course (either as a learner or as an instructor) is further exacerbated by the presence of deprecated materials from previous years. I would recommend to remove these materials, or at least relegate them to somewhere less prominent.

Because materials are spread between Youtube, Github, Kaggle and other places I may have missed, I worry also that some of these materials may not be available in the long run. This dispersion of the materials would also make it impossible to archive the entire set of materials together in something like a Zenodo DOI.

I would really love to see these materials better organized because I think that this set of materials could potentially serve as a very valuable contribution to JOSE, but I think that a major revision of the materials would be required to achieve that goal.

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See also:
kmader/Quantitative-Big-Imaging-2018#19
kmader/Quantitative-Big-Imaging-2018#20
kmader/Quantitative-Big-Imaging-2018#21
kmader/Quantitative-Big-Imaging-2018#22
kmader/Quantitative-Big-Imaging-2018#23

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Hi @kmader — 👋
Wondering here what your sense is on re-organizing the materials for better re-usability, according to @arokem's review. Thanks!

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@labarba @arokem thanks for the feedback, I definitely agree with all of it and appreciate the effort you have put in. The changes look fairly substantial and I am currently swamped with other projects. I was hoping to get to some of the issues over the coming holiday breaks.

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Hi @labarba thanks, you as well! I've made a number of the big changes already and have them as pull requests for @arokem to review when they have time.

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@arokem — I think we're waiting on you to review the latest changes. Can you give us an update? Thanks!

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Status update, @arokem ?

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Followed up by email with @arokem now.

👋 @ThomasA — I don't see any checked items on your list. Have you been able to work on this review for JOSE? Give us an update when you can. Thanks!

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Sorry for the slowness. I will comment on that PR.

Any other thoughts about the comments I made above? It looks like much of my feedback in these comments has not been incorporated yet.

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@arokem I focused on the concrete issues first because they were easier to address. As for the comments

For example, I think that many of the slide-decks are not currently useful to anyone who wasn't in the class, without additional notes that would tell us what to do with these slides. For example, the slides for the second lecture are useful as an accompaniment to the lecture that Dr. Kaestner gave, but are not necessarily useful to anyone without detailed notes from that lecture. A similar issue arises with Dr. Prummer's slides (from May 17th), but even worse, because no video is provided for this lecture. Similar can be said for many other lecture materials, that do not stand on their own, and I believe cannot currently be effectively reused, without substantial additional effort.

Unfortunately I was only able to ensure recordings on the lecture I held myself and thus the others were not done.

An overall guide in the readme that tells potential users of these materials (learners and instructors) how they should use the materials would be useful. Detailed narrative notes to accompany the lectures or at least more notes in the slides and notebooks would help.

Detailed narrative notes would be nice but the time required to remake all of the slides notes and narratives would be on the order of weeks to months (which I don't imagine having in the foreseeable future)

The profusion of materials and lack of guidance on how to proceed through the course (either as a learner or as an instructor) is further exacerbated by the presence of deprecated materials from previous years. I would recommend to remove these materials, or at least relegate them to somewhere less prominent.

The course is meant to be followed chronologically as most lectures build upon ideas in the previous, but many students manage it out of order. I kept the profusion of materials at the specific request of students who found it challenging to go between 4 years of websites. In addition, given the diversity of students in the class (ranging from computer science grad students to Art History undergrads) means it was always necessary to offer multiple parallel paths of exercises in Python (for more advanced students) and KNIME/ImageJ (for less technical ones). I tried to keep these clearly labeled but it is quite a lot to keep straight.

Because materials are spread between Youtube, Github, Kaggle and other places I may have missed, I worry also that some of these materials may not be available in the long run. This dispersion of the materials would also make it impossible to archive the entire set of materials together in something like a Zenodo DOI.

Unfortunately it would be exceptionally difficult to have a real, useful course on a single platform. All have their strengths and weaknesses and this certainly makes long run sustainability more challenging, it was done for the benefit of the students in the course today.

• Quantitative 'Big' Imaging requires hosting of datasets and computing resources which exceed what github and mybinder currently offer (thus kaggle datasets and kaggle kernels)
• Reproducibility requires that students are able to setup their own environment without being forced to put their data on a commercial site thus mybinder and repo2docker for the structure so they can recreate the exact setup everywhere and travisci ensures that the setup is valid and every notebook completes without error
• Having videos as piles of MP4 files is quite difficult to store and navigate (42 hours worth) using YouTube provides quick access, playing at 2x speed and subtitles with translations for other languages

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Here's the thing, @kmader. You have collected years of materials from your course in one GitHub repository, but this is not what JOSE was designed to publish. One of the key ideas for JOSE publications is that the material be reusable by other instructors or self-learners. Also, we write in the journal's scope:

What do you mean by "open-source educational materials"?
Examples include Jupyter notebooks or plaintext/markup language documents like LaTeX, R Markdown, and ReST for course/lesson content and associated notes, with embedded or associated code snippets/programs.
We do not mean openly available slides, lecture notes, or YouTube videos, though these may be acceptable as supplementary materials.

As a general rule, it's nearly impossible for instructors to re-use slide decks prepared by others. We also explicitly exclude multi-media content (e.g., videos), because of the focus on open source content, that can be modified, version controlled, forked and built on.

From your collection of materials, if you were to organize only the Jupyter notebooks into a coherent, self-contained learning module, that's a JOSE publication. Imagine if you were giving an intense, three-day tutorial at a conference, and you polished just the notebooks for that purpose, expecting to do fast-paced live coding, plus leave the audience with fully narrated materials to review at their own pace after the event. Those materials would be a JOSE module.

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Thanks for that info @labarba , I guess in that case it won't make sense to make this repo as it is into a JOSE publication (students still use the repo and it would not be fair to them to remove possibly useful materials to make it conform with JOSE's requirements).
I think I had originally misunderstood the exact purpose of JOSEs work and had incorrectly assumed it was meant to be open-source materials for students (all figures, examples and diagrams driven by tested, continuously integrated code rather than static slides). I had never intended for my course to be particularly useful for lecturers preparing other courses and as such it is probably a bad fit.
When I have time, I'll try to put together some of the material into a new repository just for JOSE, but I guess I can make that as a new separate submission and we can safely reject and close this one.

Thanks in any event for the helpful feedback I think it has made the material more accessible for students.

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Here's an idea: you could create a new repository with the Jupyter notebooks, polish them a little bit to make them self-contained with references out to the vids, etc. as supplementary, and then include that repo in your main course one as a GitHub module. The JOSE paper would be associated with the sub-module repo.

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👋 @kmader — I went ahead and added the paused label here. Do ping us back when you have organized a sub-set of your materials into a re-usable module. We'll be happy to review then!

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@labarba I am sorry. It seems I completely lost sight of this review a long time ago. I see @whedon just re-assigned me to the review. Does it still make sense for me to review this?

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I'm not sure why whedon did that. This submission was paused a few months back, as you can read in the thread above. But given the long time lapse, it really makes more sense to close this issue, withdraw the submission. If and when the authors re-organize their materials for a self-contained JOSE submission, they can start a new one.

Thank you for your willingness to review, @ThomasA !

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