Joss-reviews: [REVIEW]: MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues

[whedon]

Submitting author: @davidnsousa (David Sousa)
Repository: https://github.com/davidnsousa/mcsd
Version: v0.1.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @nnadeau, @mwacaan
Archive: 10.5281/zenodo.1471546

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/887b1b7792d59ea6582a4700f8ff98ad"><img src="http://joss.theoj.org/papers/887b1b7792d59ea6582a4700f8ff98ad/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/887b1b7792d59ea6582a4700f8ff98ad/status.svg)](http://joss.theoj.org/papers/887b1b7792d59ea6582a4700f8ff98ad)

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

@nnadeau & @mwacaan, 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/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

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

Review checklist for @nnadeau

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS 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 JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.1.0)?
• [x] Authorship: Has the submitting author (@davidnsousa) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

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

Review checklist for @mwacaan

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS 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 JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.1.0)?
• [x] Authorship: Has the submitting author (@davidnsousa) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

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

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @nnadeau, it looks like you're currently assigned as the reviewer for 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/joss-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/joss-reviews:

1. 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:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@nnadeau, @mwacaan this is where the review happens. Let me know if you have questions.

[Kevin-Mattheus-Moerman]

@mfroeling want to help review this package?

[nnadeau]

@davidnsousa how did Hugo A. Ferreira contribute? They are not listed in any commit history.

[davidnsousa]

@nnadeau Hugo A. Ferreira contributed to the program, tutorial, replication script and paper, but he did not contribute directly through the GitHub platform to the package maintenance. I took full responsibility on the repository.

[nnadeau]

@davidnsousa everything looks good to me! :)

Just fix the following:

• https://github.com/davidnsousa/mcsd/issues/13
• https://github.com/davidnsousa/mcsd/issues/14
• https://github.com/davidnsousa/mcsd/pull/12
• https://github.com/davidnsousa/mcsd/issues/11
• https://github.com/davidnsousa/mcsd/issues/10
• https://github.com/davidnsousa/mcsd/issues/15

[davidnsousa]

@nnadeau thank you :) these issues are all fixed!

[nnadeau]

@davidnsousa I’m at a conference in Madrid right now, but I’ll finalize everything when I’m back!

[Kevin-Mattheus-Moerman]

@mwacaan can you remind us when you are able to work on this review? Thanks! :robot:

[mwacaan]

@davidnsousa: in the paper you say: 'no simple and free open-source tools were designed and made available for researchers in this field to test their basic predictions.'
I know of at least the Camino package for Monte Carlo diffusion simulations (http://camino.cs.ucl.ac.uk/index.php?n=Tutorials.MCSimulator), but there may/must be more. Can you cite available packages in the pdf?

[Kevin-Mattheus-Moerman]

@mwacaan Thanks for your review comments. If you want to open any issues for this submission please do so here: https://github.com/davidnsousa/mcsd/issues. Thanks :rocket:

[nnadeau]

@Kevin-Mattheus-Moerman @davidnsousa everything looks good to me :)

@davidnsousa great job fixing the previous issues (especially adding testing)

[Kevin-Mattheus-Moerman]

@davidnsousa, reviewer @mwacaan posted these issues (albeit not in the correct repository), have you been able to work on these too?
https://github.com/openjournals/joss-reviews/issues/1019
https://github.com/openjournals/joss-reviews/issues/1020

[Kevin-Mattheus-Moerman]

@nnadeau are you able to tick the boxes at the top of this issue?

[davidnsousa]

@nnadeau thank you! :)

@Kevin-Mattheus-Moerman I am working on these issues.

@mwacaan thank you for your notes.

• I updated the paper.
• I fixed the name of the replication script.
• I do not see how do you get these errors. Everything runs fine locally and I have just updated the repository and the build passes . Are you running the most recent version of the .m files? Did you changed them? Could it be your MATLAB version? Thank you!

[davidnsousa]

@mwacaan is there anything I can do to help make the usage of the toolbox clear? Or is there anything more you can tell me about these errors? Thank you.

[Kevin-Mattheus-Moerman]

Reviewer @mwacaan has ticked all the boxes above and has e-mail myself and @davidnsousa the following (his first comment is about this issue: https://github.com/davidnsousa/mcsd/issues/16):

hi David and Kevin,

the joy of backwards compatibility in matlab. thanks for adding a comment David.

I ticked all boxes assuming that this automatically finalizes my review.
good luck, best,

Matthan Caan,

Thanks @mwacaan for your review.

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@davidnsousa below are some minor issues with the paper. Please work on these and regenerate the paper here by calling @whedon generate pdf.

• [x] Typo in: ....and any measures the user may want to defined, as well as...., here defined should be define.
• [x] Please add DOI's or hyperlinks where possible for all references.

[davidnsousa]

I was trying to tick the check boxes. The issues are fixed! Thank you!

[davidnsousa]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[davidnsousa]

@Kevin-Mattheus-Moerman I fixed these issues and I generated the PDF and updated zenodo.

Thank you!

[Kevin-Mattheus-Moerman]

Thanks @davidnsousa can you provide the DOI link for the updated archived version on Zenodo? Has the version/release number been changed or is it still v0.1.0?

[Kevin-Mattheus-Moerman]

@arfon once the author presents the updated version number and DOI of the archived version I recommend we accept this work in JOSS. Thanks @mwacaan and @nnadeau for your review efforts!

[ooo[bot]]

:wave: Hey @Kevin-Mattheus-Moerman...

Letting you know, @arfon is currently OOO until Monday, October 29th 2018. :heart:

[davidnsousa]

@Kevin-Mattheus-Moerman the version number has not changed. Here is the DOI link for the updated archive

Thank you

[arfon]

@whedon set 10.5281/zenodo.1471546 as archive

[whedon]

OK. 10.5281/zenodo.1471546 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/34

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/34, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/35
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00966
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

@nnadeau, @mwacaan - many thanks for your reviews here and to @Kevin-Mattheus-Moerman for editing this submission ✨

@davidnsousa - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00966 :zap: :rocket: :boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
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HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.00966/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00966/status.svg
   :target: https://doi.org/10.21105/joss.00966

This is how it will look in your documentation:

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[davidnsousa]

@Kevin-Mattheus-Moerman @nnadeau @mwacaan Thank you! :)

best,

[nnadeau]

Congrats :+1:

[nnadeau]

@arfon could you please submit this review to Publons? https://publons.com/a/1545968/

[arfon]

@arfon could you please submit this review to Publons? https://publons.com/a/1545968/

I'm not sure I know how to do this sorry :- . Any guidance/docs you might be able to point me towards here would be very welcome.

[nnadeau]

@arfon, @katyhuff introduced me to publons, maybe they have a guideline link?

[arfon]

@nnadeau - as we're not a 'partnered' journal, I think you'll need to submit this yourself: https://publons.freshdesk.com/support/solutions/articles/12000012195-how-do-i-add-reviews-to-publons-adding-reviews-

[katyhuff]

I have been adding them myself as editor of the submission (so if @nnadeau does a good job reviewing, I got to publons and note this). Since we don't send the "Thank you for your review" email that publons needs (they call it a "review receipt") I think the confirmation that a review happened comes from the editor of the submission. However, the reviewer has github notifications sent to their email, then the final thank you usually works.