[REVIEW]: NORDic: a Network-Oriented package for the Repurposing of Drugs

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@clreda@lpantano<!--end-editor-- Reviewers: @cauliyang, @sevgisu0227 Archive: 10.5281/zenodo.8355529

Status

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Markdown: [![status](https://joss.theoj.org/papers/a8173d7864bf1bc8dd074c7ce80d6d7d/status.svg)](https://joss.theoj.org/papers/a8173d7864bf1bc8dd074c7ce80d6d7d)

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

@cauliyang & @sevgisu0227, 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 @lpantano 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 @cauliyang

📝 Checklist for @sevgisu0227

editorialbot commented 10 months ago

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

OK DOIs

- 10.1038/nrm2503 is OK
- 10.1016/0022-5193(74)90172-6 is OK
- 10.1016/0022-5193(69)90015-0 is OK
- 10.48550/arXiv.2212.12756 is OK
- 10.1038/s41598-020-73147-4 is OK
- 10.1073/pnas.1610622114 is OK
- 10.1016/j.cell.2008.09.050 is OK
- 10.1073/pnas.1533293100 is OK
- 10.48550/arXiv.2111.01479 is OK
- 10.1007/978-3-031-15034-0_5 is OK
- 10.1371/journal.pcbi.1007900 is OK
- 10.48550/arXiv.2103.10070 is OK
- 10.1093/bioinformatics/btx764 is OK
- 10.1093/bioinformatics/btv305 is OK
- 10.1038/s41598-019-54180-4 is OK
- 10.1145/956750.956769 is OK
- 10.1101/2020.05.27.119016 is OK
- 10.1016/j.cell.2017.10.049 is OK
- 10.1038/nmeth.4077 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gkaa1074 is OK
- 10.5281/zenodo.7239047 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months 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/4656, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 10 months ago

@clreda I am the AEiC for this track and here to help with final steps. I have checked this review, your repository, the paper, and the archive link. Most seems in order. I only have the below points that need your attention.

On the archive:

[x] Please set the version tag for the ZENODO archive to v2.4.4, i.e. include the v as well. You can manually edit this.

On the paper:

[x] Please include the country for all affiliations.

clreda commented 10 months ago

@editorialbot generate pdf

clreda commented 10 months ago

Dear @Kevin-Mattheus-Moerman, thanks a lot for your work. Both things are done. Please let me know if something else is needed (I did the PDF generation above too soon, please consider the last generated PDF)

editorialbot commented 10 months ago

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

clreda commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

Kevin-Mattheus-Moerman commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago

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

editorialbot commented 10 months 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: Réda given-names: Clémence orcid: "https://orcid.org/0000-0003-3238-0258" - family-names: Delahaye-Duriez given-names: Andrée orcid: "https://orcid.org/0000-0003-4324-7372" doi: 10.5281/zenodo.8355529 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Réda given-names: Clémence orcid: "https://orcid.org/0000-0003-3238-0258" - family-names: Delahaye-Duriez given-names: Andrée orcid: "https://orcid.org/0000-0003-4324-7372" date-published: 2023-10-05 doi: 10.21105/joss.05532 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5532 title: "NORDic: a Network-Oriented package for the Repurposing of Drugs" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05532" volume: 8 title: "NORDic: a Network-Oriented package for the Repurposing of Drugs" ```

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 10 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 10 months 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/4657
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05532
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 10 months ago

Congratulations on this publication @clreda

Thanks for editing @lpantano! And a special thanks to the reviewers @cauliyang and @sevgisu0227

editorialbot commented 10 months ago

: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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05532/status.svg)](https://doi.org/10.21105/joss.05532)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05532">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05532/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05532/status.svg
   :target: https://doi.org/10.21105/joss.05532

This is how it will look in your documentation:

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clreda commented 10 months ago

Dear @Kevin-Mattheus-Moerman , @lpantano , @cauliyang and @sevgisu0227 thanks a lot for your help in editing and improving the paper and software!

openjournals / joss-reviews