jose-reviews [REVIEW]: The Gene School: Metagenomics

Submitting author: @koadman (Aaron Darling) Repository: https://github.com/thegeneschool/metagenomics Branch with paper.md (empty if default branch): Version: v0.0.1 Editor: @emckiernan Reviewers: @pschloss, @pvanheus, @fbidu Archive: Pending

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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) by leaving comments 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

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

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

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emckiernan know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @hughshanahan

Conflict of interest

[ ] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[ ] I confirm that I read and will adhere to the JOSE 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 (v.0.0.1)?
[ ] Authorship: Has the submitting author (@Nikoleta-v3) 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 @pschloss

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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 (v.0.0.1)?
[x] Authorship: Has the submitting author (@Nikoleta-v3) 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.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] 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

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] 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?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @erahulkulkarni

Conflict of interest

[ ] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[ ] I confirm that I read and will adhere to the JOSE 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 (v.0.0.1)?
[ ] Authorship: Has the submitting author (@Nikoleta-v3) 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 @pvanheus

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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 (v.0.0.1)?
[x] Authorship: Has the submitting author (@Nikoleta-v3) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] 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!)

[x] 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?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] 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 @fbidu

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[ ] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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 (v.0.0.1)?
[ ] Authorship: Has the submitting author (@Nikoleta-v3) 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)?

Feb 28 '20 20:02 whedon

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hughshanahan, @pschloss it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

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:

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

watching

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

Feb 28 '20 20:02 whedon

Reference check summary:

OK DOIs

- 10.1186/s13059-019-1643-1 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1038/nmeth.2066 is OK
- 10.1093/bioinformatics/btv033 is OK
- 10.7717/peerj.7359 is OK
- 10.7717/peerj.1319 is OK
- 10.1093/bioinformatics/bty560 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Feb 28 '20 20:02 whedon

:point_right: Check article proof :page_facing_up: :point_left:

Feb 28 '20 20:02 whedon

Hi @hughshanahan, @pschloss: Thank you for agreeing to review for JOSE! This is where the action happens: please work your way through the review checklist, feel free to ask questions or post comments here, and also open issues in the submission repository as needed. I'm here to help, so please let me know if you need anything. Thanks!

Feb 28 '20 20:02 emckiernan

Hi @hughshanahan, @pschloss: I know we're in a difficult time, so I don't want to pressure. But I just wanted to check in with you both about your reviews. How are things going? Anything I can help with?

Mar 23 '20 18:03 emckiernan

Hi - aagh. Sorry for dropping the ball on this. I have interviews all day tomorrow and meetings on Wednesday morning. That gives Wednesday afternoon to get after this. Please be very rude to me if I don't get it done then. Sorry again.

Mar 23 '20 21:03 hughshanahan

i'll do my best to get it up by the end of the week

Mar 24 '20 13:03 pschloss

Can @emckiernan confirm that this is the correct review template? It seems to be for software rather than for teaching materials. I was expecting something more like what is given at #78

Mar 27 '20 15:03 pschloss

Also... what is the preferred way of leaving feedback on the authors' repository? One issue with checkboxes or separate issues for each point?

Mar 27 '20 16:03 pschloss

Can @emckiernan confirm that this is the correct review template? It seems to be for software rather than for teaching materials. I was expecting something more like what is given at #78

Hi @pschloss, thanks for your question. I see your point, the review checklist is different from that provided at #78, and is missing sections like the one on pedagogy. This was automatically generated by whedon, so I'm not sure why it is different. Since this is my first time editing for JOSE, I'd like to loop in @labarba, just to make sure we're on the right track. Lorena, do you know why we have a different review template here? Thanks for any help!

Mar 30 '20 16:03 emckiernan

Also... what is the preferred way of leaving feedback on the authors' repository? One issue with checkboxes or separate issues for each point?

Hi @pschloss: The guidelines say, "Comments in the REVIEW issue should be kept brief, as much as possible, with more lengthy suggestions or requests posted as separate issues, directly in the submission repository." So I'd say, if the comments are short, you can leave something like a checklist, but if the comments are more lengthy, I'd open these as separate issues. You can link back to all of these in your review. Hope that helps!

Mar 30 '20 16:03 emckiernan

The checklist is auto-generated on the basis of the submission type chosen by the authors on the submission web form.

@koadman — do you remember choosing the submission type from the drop-down menu back when you submitted?

Mar 30 '20 16:03 labarba

what is the preferred way of leaving feedback on the authors' repository? One issue with checkboxes or separate issues for each point?

You can decide how you want to structure your feedback in the submission repository (whether to open one or several issues). But be sure to post here a link to the issue with a brief note, to create a cross-link.

Note that this Review thread will be archived together with the paper at publication time, for posterity.

Mar 30 '20 16:03 labarba

Thanks @labarba, we appreciate the help!

Mar 30 '20 16:03 emckiernan

I have posted my review in the authors' repository. I have not completed the checklist above because I'm pretty confident it's the wrong one. I may have additional comments if a different checklist is given.

Apr 01 '20 12:04 pschloss

Oh, good point. It looks like whedon posted the JOSS review checklist, rather than the JOSE checklist. @arfon @labarba ?

Apr 02 '20 21:04 kyleniemeyer

Oh, good point. It looks like whedon posted the JOSS review checklist, rather than the JOSE checklist. @arfon @labarba ?

Checking...

Apr 03 '20 00:04 arfon

@kyleniemeyer @labarba - looks like this is marked as software in the JOSE database so I think the review checklist is correct. Were you expecting the checklist for a learning module?

Apr 03 '20 00:04 arfon

@arfon yeah, I think that was a mistake that we didn't catch. This looks to be a learning module instead. Is that an easy fix, or do we just need to manually change the lists?

Apr 03 '20 03:04 kyleniemeyer

I'm afraid this is a manual change to the lists so I think you are as well-positioned as I am to make this change :-)

Apr 03 '20 12:04 arfon

I have manually changed the review checklists. @pschloss — you'll have to go back and re-check items, I'm afraid.

Apr 03 '20 13:04 labarba

I've completed the checklist. I think it matches what I have written in my review in the repository.

Apr 03 '20 16:04 pschloss

Hi @hughshanahan, just checking in about your review, thanks!

Apr 07 '20 22:04 emckiernan

Hi @hughshanahan, just checking in about your review, thanks!

Hi @hughshanahan, just checking in again, thanks!

Apr 13 '20 16:04 emckiernan

@whedon remove @hughshanahan as reviewer

May 13 '20 17:05 emckiernan

OK, @hughshanahan is no longer a reviewer

May 13 '20 17:05 whedon

Hi @erahulkulkarni! You signed up to review for JOSE. Would you like to contribute a review for this submission? The title is "The Gene School: Metagenomics". Please let me know if you're available and willing. Thanks!

May 13 '20 17:05 emckiernan

Good Morning Erin C. McKiernan,

I am a bit rusty on BioInformatics since it has been a long time I have worked on any projects.

So, I may not be the best match at present.

If it is still okay, please let me know.

Thanks and Regards, Rahul Kulkarni

On Wed, May 13, 2020 at 11:06 PM Erin C. McKiernan [email protected] wrote:

Hi @erahulkulkarni https://github.com/erahulkulkarni! You signed up to review for JOSE. Would you like to contribute a review for this submission? The title is "The Gene School: Metagenomics". Please let me know if you're available and willing. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/79#issuecomment-628140067, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBG2GORM4G3K2BKCIXGENTRRLLCVANCNFSM4K53OZEA .

May 14 '20 10:05 erahulkulkarni

Hi @erahulkulkarni, thanks for your response and apologies for my slow reply! If you're still willing, it would be great to have you review, even if rusty :). I think one of the most important things is to evaluate that all the documentation of the software and educational tools described is complete and makes sense to you. In my opinion, the didactic materials should be as clear as possible, even to others without in-depth expertise in the area. Hope that helps, and thanks in advance for considering!

May 19 '20 18:05 emckiernan

Good Morning Erin C. McKiernan,

No worries.

Okay then, I will check rules / documentation of review and a give a try. Thank You.

Thanks and Regards, Rahul Kulkarni

On Wed, May 20, 2020 at 12:16 AM Erin C. McKiernan [email protected] wrote:

Hi @erahulkulkarni https://github.com/erahulkulkarni, thanks for your response and apologies for my slow reply! If you're still willing, it would be great to have you review, even if rusty :). I think one of the most important things is to evaluate that all the documentation of the software and educational tools described is complete and makes sense to you. In my opinion, the didactic materials should be as clear as possible, even to someone without in-depth expertise in the area. Hope that helps, and thanks in advance for considering!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/79#issuecomment-631010340, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBG2GKSX3IO434BUM5XRFDRSLHYRANCNFSM4K53OZEA .

May 20 '20 15:05 erahulkulkarni