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[REVIEW]: Tutorial for Developing Image-Guided Intervention Modules Using 3D Slicer #46

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whedon opened this Issue Feb 26, 2019 · 9 comments

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whedon commented Feb 26, 2019

Submitting author: @lgroves6 (Leah Groves)
Repository: https://github.com/lgroves6/IGTTutorialWebsite
Version: v1.0.0
Editor: @juanklopper
Reviewer: @jcfr, @fedorov
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://jose.theoj.org/papers/6ac66d8b1a941caee5dd8030929b1f3a"><img src="http://jose.theoj.org/papers/6ac66d8b1a941caee5dd8030929b1f3a/status.svg"></a>
Markdown: [![status](http://jose.theoj.org/papers/6ac66d8b1a941caee5dd8030929b1f3a/status.svg)](http://jose.theoj.org/papers/6ac66d8b1a941caee5dd8030929b1f3a)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@jcfr & @fedorov, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://jose.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @juanklopper know.

Review checklist for @jcfr

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source for this learning module available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
  • Version: Does the release version given match the repository release (v1.0.0)?
  • Authorship: Has the submitting author (@lgroves6) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • Installation instructions: Is there a clearly stated list of dependencies?
  • Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

  • Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
  • Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Does the paper clearly state the need for this module and who the target audience is?
  • Description: Does the paper describe the learning materials and sequence?
  • Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
  • Could someone else teach with this module, given the right expertise?
  • Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @fedorov

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source for this learning module available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
  • Version: Does the release version given match the repository release (v1.0.0)?
  • Authorship: Has the submitting author (@lgroves6) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • Installation instructions: Is there a clearly stated list of dependencies?
  • Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

  • Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
  • Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Does the paper clearly state the need for this module and who the target audience is?
  • Description: Does the paper describe the learning materials and sequence?
  • Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
  • Could someone else teach with this module, given the right expertise?
  • Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Feb 26, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jcfr, 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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

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whedon commented Feb 26, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 26, 2019

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labarba commented Feb 26, 2019

👋 @jcfr, @fedorov — Thanks for agreeing to review! This is where the action happens. You have a review checklist above, but you should feel free to add any comments in this thread. You may also open issues in the submission repository, as needed, and mention them here, so we get a cross-link.

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labarba commented Feb 26, 2019

@lgroves6 — At any point, after you make changes to the paper, you can run the command @whedon generate pdf to get a new pre-print here.

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fedorov commented Feb 27, 2019

@labarba can you confirm this submission is within the scope of this publishing platform?

Reading from the scope of it here http://jose.theoj.org/about

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. In addition, course syllabi by themselves are not suitable for submission (Syllabus may be more appropriate).

tl;dr: your course or lesson content must contain or use code to teach. We are not focused exclusively on learning to code, but coding to learn.

The present submission is a web site with the instructions, YouTube videos, etc.

As I was browsing over other issues in this repo, I also came across an earlier submission (#25), which looked interesting to me, so I read through the discussion thread. It is somewhat similar, since it is a collection of non-code-like educational materials, where you @labarba specifically seem to imply that it is out of scope of this platform, see #25 (comment).

Please advice.

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fedorov commented Mar 20, 2019

@labarba can you please let us know your response to the question in the previous comment left 3 weeks ago?

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labarba commented Mar 21, 2019

Indeed, if the materials submitted for review consist on multi-media instructional resources and a website, that is not what JOSE is looking to publish. We are looking for re-usable and complete learning modules that use "coding to learn" (a.k.a. computational thinking). Any videos or slide decks are only considered supplementary to a JOSE publication.

JOSE publishes tutorials with programming as a major component, fully narrated and usable for self-learners or other instructors.

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labarba commented Mar 22, 2019

@juanklopper — I see that in the Pre-Review issue we already had an exchange about the type of material submitted here, and if it was within scope for JOSE. Nevertheless, we started the review. @fedorov now raises again the in-scope question, having explored the materials further.

I had a bit of trouble finding the actual website, as the submission repository has not link to it, although it is in the paper. Exploring a bit more now, I see a narrative, with figures and screenshots of an application. The material doesn't use programming, it looks like, although it includes some demos for developing scripted modules for the 3D slicer.

After having this deeper look into the materials presented, I do think this submission is out of scope for JOSE. What do you think, @juanklopper ?

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