[REVIEW]: EduCortex: browser-based 3D brain visualization of fMRI meta-analysis maps #75

whedon · 2020-02-05T14:52:28Z

Submitting author: @PaulScotti (Paul Scotti)
Repository: https://github.com/PaulScotti/EduCortex
Version: v1.1
Editor: @magsol
Reviewers: @tliu23, @TomDonoghue
Archive: 10.5281/zenodo.3732375

Status

Status badge code:

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Markdown: [![status](https://jose.theoj.org/papers/9c6a6a00a0c2d68f1e896de9e59471ea/status.svg)](https://jose.theoj.org/papers/9c6a6a00a0c2d68f1e896de9e59471ea)

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

@tliu23 & @TomDonoghue & @arokem, 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
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @magsol know.

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

Review checklist for @tliu23

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 code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: v1.1
Authorship: Has the submitting author (@PaulScotti) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state the need for this software and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies? (Ideally these should be handled with an automated package management solution.)
Example usage: Do the authors include examples of how to use the software?
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Tests: Are there automated tests or manual steps described so that the function of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state the need for this software and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @TomDonoghue

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 code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: v1.1
Authorship: Has the submitting author (@PaulScotti) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state the need for this software and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies? (Ideally these should be handled with an automated package management solution.)
Example usage: Do the authors include examples of how to use the software?
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Tests: Are there automated tests or manual steps described so that the function of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state the need for this software and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @arokem

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 code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: v1.1
Authorship: Has the submitting author (@PaulScotti) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state the need for this software and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies? (Ideally these should be handled with an automated package management solution.)
Example usage: Do the authors include examples of how to use the software?
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Tests: Are there automated tests or manual steps described so that the function of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state the need for this software and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

The text was updated successfully, but these errors were encountered:

whedon · 2020-02-05T14:52:32Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tliu23, @TomDonoghue, @arokem it looks like you're currently assigned to review 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:

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

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

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

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

@whedon generate pdf

whedon · 2020-02-05T14:54:42Z

👉 Check article proof 📄 👈

whedon · 2020-02-05T14:55:57Z

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.3389/fninf.2015.00023 may be missing for title: Pycortex: an interactive surface visualizer for fMRI
- https://doi.org/10.1016/s1364-6613(03)00134-7 may be missing for title: The visual word form area: expertise for reading in the fusiform gyrus

INVALID DOIs

- None

magsol · 2020-02-12T17:30:20Z

Hi @TomDonoghue and @tliu23, wanted to check in on how the review is going and see if there was anything you needed!

TomDonoghue · 2020-02-16T02:03:36Z

Sorry for being a little slow - had a busy week last week - but should be able to do the review in the next couple days, and don't think I need anything in particular for now! Thanks!

magsol · 2020-03-03T17:09:41Z

Hi @TomDonoghue and @tliu23, I'd really like to wrap this review up soon. Please let me know if you need anything in the meantime. Thanks!

tliu23 · 2020-03-04T14:00:18Z

Went through the lists and checked the ones.

tliu23 · 2020-03-04T14:01:49Z

Thanks for the reminder. Just went through the list and checked the ones I am more certain. Tianming

…

On Tue, Mar 3, 2020 at 12:09 PM Shannon ***@***.***> wrote: Hi @TomDonoghue <https://github.com/TomDonoghue> and @tliu23 <https://github.com/tliu23>, I'd really like to wrap this review up soon. Please let me know if you need anything in the meantime. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#75?email_source=notifications&email_token=AD3OMDHQ4AF5J76KPJJDOTTRFU2VNA5CNFSM4KQMN4TKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENUKTWA#issuecomment-594061784>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3OMDGQ5QXYQOSAPQF2DD3RFU2VNANCNFSM4KQMN4TA> .

-- Tianming Liu Distinguished Research Professor Department of Computer Science & Bioimaging Research Center & Institute of Bioinformatics & Neuroscience PhD Program & Institute of Artificial Intelligence The University of Georgia Boyd GSRC 420 Athens, GA 30602 Phone 706-542-3478 Email: tliu@cs.uga.edu <tliu@uga.edu> Web: http://cobweb.cs.uga.edu/~tliu/

magsol · 2020-03-04T15:54:49Z

Thanks @tliu23, let me know when you think you can check off the last couple items.

tliu23 · 2020-03-04T16:37:34Z

Done, thanks.

tliu23 · 2020-03-04T16:37:56Z

Done.

…

On Wed, Mar 4, 2020 at 10:54 AM Shannon ***@***.***> wrote: Thanks @tliu23 <https://github.com/tliu23>, let me know when you think you can check off the last couple items. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#75?email_source=notifications&email_token=AD3OMDGUWOWMLYTMZYV73LTRFZ2UTA5CNFSM4KQMN4TKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENYTLIQ#issuecomment-594621858>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3OMDBKZTGMVTYZYOZMYMLRFZ2UTANCNFSM4KQMN4TA> .

-- Tianming Liu Distinguished Research Professor Department of Computer Science & Bioimaging Research Center & Institute of Bioinformatics & Neuroscience PhD Program & Institute of Artificial Intelligence The University of Georgia Boyd GSRC 420 Athens, GA 30602 Phone 706-542-3478 Email: tliu@cs.uga.edu <tliu@uga.edu> Web: http://cobweb.cs.uga.edu/~tliu/

magsol · 2020-03-04T16:39:03Z

Awesome, thanks @tliu23. Did you have any final comments for the authors?

tliu23 · 2020-03-04T16:40:08Z

No.

…

On Wed, Mar 4, 2020 at 11:39 AM Shannon ***@***.***> wrote: Awesome, thanks @tliu23 <https://github.com/tliu23>. Did you have any final comments for the authors? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#75?email_source=notifications&email_token=AD3OMDDY6APGDKP5YZDBXVLRFZ72RA5CNFSM4KQMN4TKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENY2GII#issuecomment-594649889>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3OMDAT6TEG6JNWAMFU7UDRFZ72RANCNFSM4KQMN4TA> .

-- Tianming Liu Distinguished Research Professor Department of Computer Science & Bioimaging Research Center & Institute of Bioinformatics & Neuroscience PhD Program & Institute of Artificial Intelligence The University of Georgia Boyd GSRC 420 Athens, GA 30602 Phone 706-542-3478 Email: tliu@cs.uga.edu <tliu@uga.edu> Web: http://cobweb.cs.uga.edu/~tliu/

magsol · 2020-03-04T16:40:44Z

Great, thanks.

@TomDonoghue, let me know when you'd be able to get to the review. Would love to wrap this up soon.

TomDonoghue · 2020-03-04T16:51:42Z

@magsol : I'm very sorry for the delay - I will get to this today!

Edit: been working through the project (looks super cool), will consolidate my thoughts and post comments and finish review soon.

whedon · 2020-03-28T17:37:08Z

OK, @arokem is no longer a reviewer

magsol · 2020-03-28T17:37:59Z

@whedon generate pdf

whedon · 2020-03-28T17:39:25Z

👉 Check article proof 📄 👈

magsol · 2020-03-28T17:43:54Z

Sorry for the delay--university changes around COVID-19 have upended my schedule from its roots, though I'm sure I don't have to explain that to anyone here.

Thanks @tliu23 and @TomDonoghue for your reviews, and especially Tom for the insightful comments and feedback. This was a lot of fun to read, and super awesome that this came out of Neurohackademy; it's such a phenomenal annual workshop/meeting.

To finalize EduCortex for publication, @PaulScotti I need you to make a tagged release & archive of the artifact. Once that's done, report version number and DOI in this thread, and we can take it from there.

PaulScotti · 2020-03-29T13:07:47Z

v1.1: https://github.com/PaulScotti/educortex/releases/tag/v1.1
archive: https://doi.org/10.5281/zenodo.3732375

Huge thanks to @magsol @TomDonoghue and @tliu23 for their time and effort spent facilitating this review process, I'm very thankful that this journal exists to support projects like this.

magsol · 2020-03-30T00:27:04Z

@whedon set 10.5281/zenodo.3732375 as archive

whedon · 2020-03-30T00:27:08Z

OK. 10.5281/zenodo.3732375 is the archive.

magsol · 2020-03-30T00:27:48Z

@whedon set v1.1 as version

whedon · 2020-03-30T00:27:53Z

OK. v1.1 is the version.

magsol · 2020-03-30T00:28:15Z

@whedon accept

whedon · 2020-03-30T00:28:18Z

Attempting dry run of processing paper acceptance...

whedon · 2020-03-30T00:30:03Z

👋 @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/jose-papers#47

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#47, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

magsol · 2020-04-03T16:48:10Z

Hi @openjournals/jose-eics , whenever you get a chance, please give @PaulScotti 's submission here a final yay/nay!

labarba · 2020-04-04T11:33:05Z

@PaulScotti — Could you edit the metadata of the Zenodo deposit so the title and author list matches the paper? Thanks!

PaulScotti · 2020-04-04T11:42:34Z

@labarba I corrected the author names/affiliations and the title of the Zenodo deposit, are there other metadata that I should correct?

labarba · 2020-04-04T12:06:18Z

@whedon accept deposit=true

whedon · 2020-04-04T12:06:21Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2020-04-04T12:08:20Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSE! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00075 jose-papers#48
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/jose.00075
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba · 2020-04-04T12:17:22Z

Congratulations, @PaulScotti, your JOSE paper is published! 🚀

Huge thanks to our editor: @magsol, and the reviewers: @tliu23, @TomDonoghue — we couldn't do this without you 🙏

labarba · 2020-04-04T12:21:05Z

https://twitter.com/JOSE_TheOJ/status/1246412103361191936

whedon · 2020-04-04T12:21:09Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://jose.theoj.org/papers/10.21105/jose.00075/status.svg)](https://doi.org/10.21105/jose.00075)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00075">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00075/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00075/status.svg
   :target: https://doi.org/10.21105/jose.00075

This is how it will look in your documentation:

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Journal of Open Source Education is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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whedon added the review label Feb 5, 2020

whedon assigned magsol Feb 5, 2020

whedon mentioned this issue Feb 5, 2020

[PRE REVIEW]: EduCortex: browser-based 3D brain visualization of fMRI meta-analysis maps #72

Closed

whedon assigned arokem, tliu23 and TomDonoghue Feb 6, 2020

tliu23 closed this as completed Mar 4, 2020

tliu23 reopened this Mar 4, 2020

tliu23 closed this as completed Mar 4, 2020

magsol reopened this Mar 4, 2020

tliu23 closed this as completed Mar 4, 2020

magsol reopened this Mar 4, 2020

This was referenced Mar 5, 2020

Interface Bug: 'Data' selector in the top left interaction box PaulScotti/educortex#5

Closed

Install Instructions PaulScotti/educortex#6

Closed

Suggestion: Add Versioning PaulScotti/educortex#7

Closed

whedon assigned magsol and unassigned TomDonoghue and tliu23 Mar 28, 2020

whedon assigned tliu23 and TomDonoghue Mar 28, 2020

whedon added the recommend-accept Papers recommended for acceptance in JOSE. label Mar 30, 2020

whedon added accepted published Papers published in JOSE labels Apr 4, 2020

labarba closed this as completed Apr 4, 2020

[REVIEW]: EduCortex: browser-based 3D brain visualization of fMRI meta-analysis maps #75

[REVIEW]: EduCortex: browser-based 3D brain visualization of fMRI meta-analysis maps #75

whedon commented Feb 5, 2020 •

edited

whedon commented Feb 5, 2020

whedon commented Feb 5, 2020

whedon commented Feb 5, 2020

magsol commented Feb 12, 2020

TomDonoghue commented Feb 16, 2020

magsol commented Mar 3, 2020

tliu23 commented Mar 4, 2020

tliu23 commented Mar 4, 2020 via email

magsol commented Mar 4, 2020

tliu23 commented Mar 4, 2020

tliu23 commented Mar 4, 2020 via email

magsol commented Mar 4, 2020

tliu23 commented Mar 4, 2020 via email

magsol commented Mar 4, 2020

TomDonoghue commented Mar 4, 2020 •

edited

whedon commented Mar 28, 2020

magsol commented Mar 28, 2020

whedon commented Mar 28, 2020

magsol commented Mar 28, 2020

PaulScotti commented Mar 29, 2020

magsol commented Mar 30, 2020

whedon commented Mar 30, 2020

magsol commented Mar 30, 2020

whedon commented Mar 30, 2020

magsol commented Mar 30, 2020

whedon commented Mar 30, 2020

whedon commented Mar 30, 2020

magsol commented Apr 3, 2020

labarba commented Apr 4, 2020

PaulScotti commented Apr 4, 2020

labarba commented Apr 4, 2020

whedon commented Apr 4, 2020

whedon commented Apr 4, 2020

labarba commented Apr 4, 2020

labarba commented Apr 4, 2020

whedon commented Apr 4, 2020

[REVIEW]: EduCortex: browser-based 3D brain visualization of fMRI meta-analysis maps #75

[REVIEW]: EduCortex: browser-based 3D brain visualization of fMRI meta-analysis maps #75

Comments

whedon commented Feb 5, 2020 • edited

Status

Reviewer instructions & questions

Review checklist for @tliu23

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @TomDonoghue

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @arokem

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Feb 5, 2020

whedon commented Feb 5, 2020

whedon commented Feb 5, 2020

magsol commented Feb 12, 2020

TomDonoghue commented Feb 16, 2020

magsol commented Mar 3, 2020

tliu23 commented Mar 4, 2020

tliu23 commented Mar 4, 2020 via email

magsol commented Mar 4, 2020

tliu23 commented Mar 4, 2020

tliu23 commented Mar 4, 2020 via email

magsol commented Mar 4, 2020

tliu23 commented Mar 4, 2020 via email

magsol commented Mar 4, 2020

TomDonoghue commented Mar 4, 2020 • edited

whedon commented Mar 28, 2020

magsol commented Mar 28, 2020

whedon commented Mar 28, 2020

magsol commented Mar 28, 2020

PaulScotti commented Mar 29, 2020

magsol commented Mar 30, 2020

whedon commented Mar 30, 2020

magsol commented Mar 30, 2020

whedon commented Mar 30, 2020

magsol commented Mar 30, 2020

whedon commented Mar 30, 2020

whedon commented Mar 30, 2020

magsol commented Apr 3, 2020

labarba commented Apr 4, 2020

PaulScotti commented Apr 4, 2020

labarba commented Apr 4, 2020

whedon commented Apr 4, 2020

whedon commented Apr 4, 2020

labarba commented Apr 4, 2020

labarba commented Apr 4, 2020

whedon commented Apr 4, 2020

whedon commented Feb 5, 2020 •

edited

TomDonoghue commented Mar 4, 2020 •

edited