[REVIEW]: Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes.

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@JeanMainguy@arfon<!--end-editor-- Reviewers: @lskatz, @beardymcjohnface Archive: 10.5281/zenodo.13789302

Status

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Markdown: [![status](https://joss.theoj.org/papers/ad304709d59f1a51a31614393b09ba2b/status.svg)](https://joss.theoj.org/papers/ad304709d59f1a51a31614393b09ba2b)

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

@lskatz & @beardymcjohnface, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @lskatz

📝 Checklist for @beardymcjohnface

editorialbot commented 5 months ago

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editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1189.8 files/s, 155400.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            951            579           1875
Markdown                        10            249              0            459
TeX                              1             25              0            185
YAML                             6             40             44            172
TOML                             1              7              4             57
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            36           1284            635           2783
-------------------------------------------------------------------------------

Commit count by author:

   120  JeanMainguy
    79  Jean Mainguy

editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 850

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 5 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-019-1058-x is OK
- 10.1038/s42003-021-02112-2 is OK
- 10.7717/peerj.7359 is OK
- 10.1038/nmeth.3103 is OK
- 10.1038/s41587-020-00777-4 is OK
- 10.1038/s41564-018-0171-1 is OK
- 10.1093/bioinformatics/btac694 is OK
- 10.1186/s40168-018-0541-1 is OK
- 10.1038/s41592-022-01431-4 is OK
- 10.1101/gr.186072.114 is OK
- 10.1038/s41592-023-01940-w is OK
- 10.1038/nmeth.3176 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/s41592-018-0046-7 is OK

MISSING DOIs

- No DOI given, and none found for title: MetagWGS, a complete workflow to analyse metagenom...

INVALID DOIs

- None

editorialbot commented 5 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 5 months ago

@lskatz, @beardymcjohnface – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6782 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

lskatz commented 5 months ago

Review checklist for @lskatz

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/genotoul-bioinfo/Binette?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@JeanMainguy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

beardymcjohnface commented 5 months ago

Review checklist for @beardymcjohnface

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/genotoul-bioinfo/Binette?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@JeanMainguy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

lskatz commented 4 months ago

Some general comments on the paper

Line 42: why is the weight set as 2?
Clarity on line 45: currently is " rather than CheckM1 as in the metaWRAP pipeline" but maybe " rather than CheckM1, which is what the metaWRAP pipeline uses"
Line 96: does JOSS allow for in preparation citations? (might be a question for the editor)

lskatz commented 4 months ago

Any questions/concerns please let @arfon know.

@arfon does JOSS allow for in preparation citations?

arfon commented 4 months ago

@arfon does JOSS allow for in preparation citations?

I think that's fine.

Kevin-Mattheus-Moerman commented 4 months ago

@lskatz I would only add that if you can post a pre-print for these and cite these that would be preferred.

JeanMainguy commented 3 months ago

Hello, Thanks for the feedbacks.

* Line 42: why is the weight set as 2?

The contamination weight is set to 2 by default based on tests conducted with the CAMI dataset. I experimented with various weights and selected the optimal one. From my observations, this parameter does not have a huge impact on the number of high-quality bins. The weight is adjustable and depends on the user's tolerance for contamination in the resulting bins. It can be increased if the user is uncomfortable with some contamination in the final bins and wants to minimize it as much as possible.

* Clarity on line 45: currently is " rather than CheckM1 as in the metaWRAP pipeline" but maybe " rather than CheckM1, which is what the metaWRAP pipeline uses"

I've made the change. Thanks.

* Line 96: does JOSS allow for in preparation citations? (might be a question for the editor)

We are almost ready to submit the metagWGS paper. We will post it as a preprint and cite it accordingly as suggested by @Kevin-Mattheus-Moerman.

lskatz commented 3 months ago

@JeanMainguy thank you! I think after those comments, we just need example usage and then I'm all set to suggest acceptance.

JeanMainguy commented 3 months ago

Ok, great ! I'm working on the tutorial, but I'm having a bit of trouble figuring out the right dataset size. I want it to run on a laptop without taking forever, but still give some interesting results. But anyway, I'll try to finish it soon !

arfon commented 2 months ago

:wave: @JeanMainguy – just checking in again here to see how things are going?

JeanMainguy commented 2 months ago

Hello, I'm almost finished with the tutorial and plan to complete it by the end of this week!

JeanMainguy commented 2 months ago

Hi, I have added the tutorial to Binette documentation. You can check it out here: https://binette.readthedocs.io/en/latest/tutorial/tutorial_main.html

We plan to submit the metagWGS paper next week (hopefully) and will also upload the manuscript to BioRxiv at that time. I’ll keep you updated once the submission is complete and when I’ve updated the paper references accordingly.

lskatz commented 2 months ago

The tutorial is well done!

@Kevin-Mattheus-Moerman This completes my checklist.

arfon commented 2 months ago

Thanks for confirming @lskatz. @beardymcjohnface – given your checklist, I suspect this is a 'yes', but could you confirm that you are recommending we publish this submission?

beardymcjohnface commented 2 months ago

yes!

arfon commented 2 months ago

@JeanMainguy – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors
I can then move forward with accepting the submission.

JeanMainguy commented 2 months ago

I'll let you know once everything is in place.Thank you

JeanMainguy commented 1 month ago

Hi @arfon , I just released a new version of Binette and published the archive on zenodo : https://doi.org/10.5281/zenodo.13789302

JeanMainguy commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1038/s41586-019-1058-x is OK
- 10.1038/s42003-021-02112-2 is OK
- 10.7717/peerj.7359 is OK
- 10.1038/nmeth.3103 is OK
- 10.1038/s41587-020-00777-4 is OK
- 10.1038/s41564-018-0171-1 is OK
- 10.1093/bioinformatics/btac694 is OK
- 10.1186/s40168-018-0541-1 is OK
- 10.1038/s41592-022-01431-4 is OK
- 10.1101/gr.186072.114 is OK
- 10.1038/s41592-023-01940-w is OK
- 10.1038/nmeth.3176 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1101/2024.09.13.612854 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/s41592-018-0046-7 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

JeanMainguy commented 1 month ago

Hi @arfon,

I forgot to mention that I’ve completed a final read-through of the paper before release and updated the metagWGS reference with its preprint DOI, as suggested earlier.

Is there anything else you need from my side to move this forward?

Thanks!

arfon commented 1 month ago

@editorialbot set 10.5281/zenodo.13789302 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13789302

arfon commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1038/s41586-019-1058-x is OK
- 10.1038/s42003-021-02112-2 is OK
- 10.7717/peerj.7359 is OK
- 10.1038/nmeth.3103 is OK
- 10.1038/s41587-020-00777-4 is OK
- 10.1038/s41564-018-0171-1 is OK
- 10.1093/bioinformatics/btac694 is OK
- 10.1186/s40168-018-0541-1 is OK
- 10.1038/s41592-022-01431-4 is OK
- 10.1101/gr.186072.114 is OK
- 10.1038/s41592-023-01940-w is OK
- 10.1038/nmeth.3176 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1101/2024.09.13.612854 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/s41592-018-0046-7 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 month ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5958, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 1 month ago

@editorialbot accept

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Mainguy given-names: Jean orcid: "https://orcid.org/0009-0006-9160-9744" - family-names: Hoede given-names: Claire orcid: "https://orcid.org/0000-0001-5054-7731" contact: - family-names: Hoede given-names: Claire orcid: "https://orcid.org/0000-0001-5054-7731" doi: 10.5281/zenodo.13789302 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Mainguy given-names: Jean orcid: "https://orcid.org/0009-0006-9160-9744" - family-names: Hoede given-names: Claire orcid: "https://orcid.org/0000-0001-5054-7731" date-published: 2024-10-05 doi: 10.21105/joss.06782 issn: 2475-9066 issue: 102 journal: Journal of Open Source Software publisher: name: Open Journals start: 6782 title: "Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes." type: article url: "https://joss.theoj.org/papers/10.21105/joss.06782" volume: 9 title: "Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes." ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 1 month ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 month ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5970
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06782
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 1 month ago

@lskatz, @beardymcjohnface – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@JeanMainguy – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 1 month ago

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