[REVIEW]: NOMAD: A distributed web-based platform for managing materials science research data

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@markus1978@zhubonan<!--end-editor-- Reviewers: @arosen93, @berquist, @sgbaird Archive: 10.5281/zenodo.8366163

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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:

zhubonan commented 10 months ago

@editorialbot set 10.5281/zenodo.8366163 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.8366163

zhubonan commented 10 months ago

@editorialbot set 1.2.1 as version

editorialbot commented 10 months ago

Done! version is now 1.2.1

zhubonan commented 10 months ago

@editorialbot generate pdf

zhubonan commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.1038/s41586-022-04501-x is OK
- 10.1038/s41597-023-02501-8 is OK
- 10.1038/s41597-021-00974-z is OK
- 10.1063/1.4812323 is OK
- 10.1007/s11837-013-0755-4 is OK
- 10.1016/j.commatsci.2012.02.005 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1038/s41524-018-0107-6 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1107/S1600576714027575 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.48550/arXiv.1805.05039 is OK
- 10.1038/sdata.2018.53 is OK
- 10.1038/s41524-017-0048-5 is OK
- 10.1038/s41524-022-00935-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

zhubonan commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.1038/s41586-022-04501-x is OK
- 10.1038/s41597-023-02501-8 is OK
- 10.1038/s41597-021-00974-z is OK
- 10.1063/1.4812323 is OK
- 10.1007/s11837-013-0755-4 is OK
- 10.1016/j.commatsci.2012.02.005 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1038/s41524-018-0107-6 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1107/S1600576714027575 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.48550/arXiv.1805.05039 is OK
- 10.1038/sdata.2018.53 is OK
- 10.1038/s41524-017-0048-5 is OK
- 10.1038/s41524-022-00935-z 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/4619, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

markus1978 commented 10 months ago

@zhubonan Before you issue the final command, I would like to circulate the final proof once more with the other authors. I will report back Oct 4th 2023.

zhubonan commented 10 months ago

No problem. Actually, we are waiting for the associate editor in chief to issue final acceptance.

Kevin-Mattheus-Moerman commented 10 months ago

@editorialbot set v1.2.1 as version

editorialbot commented 10 months ago

Done! version is now v1.2.1

Kevin-Mattheus-Moerman commented 10 months ago

@zhubonan thanks for editing here. Note for the future, the repository version tag should be fully matched and is here v1.2.1 (so including the v). The ZENODO archive should then say Version v1.2.1 (since their word "version" should really say "version tag"). So I'll ask the authors to update the archive link to which says 1.2.1 at the moment.

Kevin-Mattheus-Moerman commented 10 months ago

@markus1978 I am the AEiC for this track and here to help process final steps. I have check this review, the repository, the archive link and the paper. Most seems in order but below are some minor points that needs your attention:

[x] Please update the ZENODO archive listed version to v1.2.1.
[x] You mention the authors are doing a final review. Please let me know when this is finished, so we can proceed here.

Kevin-Mattheus-Moerman commented 9 months ago

@zhubonan :wave:

zhubonan commented 9 months ago

Ah I see. @markus1978 could you please update the zenodo version tag? Should be able to do so without reupload I think.

zhubonan commented 9 months ago

~~Or the alternative is to re-release with a 1.2.1 tag?~~

Kevin-Mattheus-Moerman commented 9 months ago

@zhubonan sorry I meant to tag @markus1978. We'll wait for the authors now to make those changes.

markus1978 commented 9 months ago

@Kevin-Mattheus-Moerman

I comited a new version of the paper with spelling/grammar things, and one affiliation change.
I updated the version on zenodo and added the "v".

I am sorry for the late changes to the paper, I hope this does not cause too many issues. But i think all the co-authors are now happy and we can proceed.

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 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 9 months ago

@markus1978 thanks for making those changes. I have some more minor points below:

[x] Since the acronym (ELN) is not used, you can remove it from the text.
[x] Check ... following the instruction ... which should perhaps be ... following the instructions ...
[x] Your text mentions: NOMAD Oasis can be used freely as per our OSI license..., I recommend that you actually mention the license you use (Apache 2.0).
[x] In fact, given the above two points I would recommend to rephrase the following sentence to target the above: NOMAD Oasis can be used freely as per our OSI license following the instruction in the [NOMAD documentation](https://nomad-lab.eu/docs). to something like: NOMAD Oasis can be used freely, is available open source under the [Apache License 2.0](https://github.com/nomad-coe/nomad/blob/develop/LICENSE), and detailed instructions are available in the [NOMAD documentation](https://nomad-lab.eu/docs).

markus1978 commented 9 months ago

@Kevin-Mattheus-Moerman thanks you very much for your suggestions. We now follow your suggestion for the last 3 points. For the first point, I would like to keep the acronym if possible. "ELN" is so prevalent in our community that for many readers "ELN" is more recognisable than "electronic lab notebook".

zhubonan commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

zhubonan commented 9 months ago

Thanks for making the changes. I think the use of ELN is probably OK here. Pinging @Kevin-Mattheus-Moerman again.

Kevin-Mattheus-Moerman commented 9 months ago

@markus1978 Apologies for the delay in processing this. Thanks for implementing those final changes. I'll now proceed to accept this work for JOSS.

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot accept

editorialbot commented 9 months ago

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

editorialbot commented 9 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: - email: markus.scheidgen@physik.hu-berlin.de family-names: Scheidgen given-names: Markus orcid: "https://orcid.org/0000-0002-8038-2277" - email: lauri.himanen@gmail.com family-names: Himanen given-names: Lauri orcid: "https://orcid.org/0000-0002-3130-8193" - email: alvin.noe.ladines@physik.hu-berlin.de family-names: Ladines given-names: Alvin Noe orcid: "https://orcid.org/0000-0003-0077-2097" - email: david.sikter@physik.hu-berlin.de family-names: Sikter given-names: David orcid: "https://orcid.org/0000-0002-2102-7160" - email: mohammad.nakhaee@physik.hu-berlin.de family-names: Nakhaee given-names: Mohammad orcid: "https://orcid.org/0000-0003-4146-0129" - email: adam@fekete.co.uk family-names: Fekete given-names: Ádám orcid: "https://orcid.org/0000-0002-6263-897X" - email: theodore.chang@physik.hu-berlin.de family-names: Chang given-names: Theodore orcid: "https://orcid.org/0000-0002-4911-0230" - email: amir.golparvar@physik.hu-berlin.de family-names: Golparvar given-names: Amir orcid: "https://orcid.org/0000-0002-2412-6615" - email: jose.marquez@physik.hu-berlin.de family-names: Márquez given-names: José A. orcid: "https://orcid.org/0000-0002-8173-2566" - email: sandor.brockhauser@physik.hu-berlin.de family-names: Brockhauser given-names: Sandor orcid: "https://orcid.org/0000-0002-9700-4803" - email: sebastian.brueckner@ikz-berlin.de family-names: Brückner given-names: Sebastian orcid: "https://orcid.org/0000-0002-5969-847X" - email: luca.ghiringhelli@physik.hu-berlin.de family-names: Ghiringhelli given-names: Luca M. orcid: "https://orcid.org/0000-0001-5099-3029" - email: felix.dietrich@tum.de family-names: Dietrich given-names: Felix orcid: "https://orcid.org/0000-0002-2906-1769" - email: d.lehmberg@tum.de family-names: Lehmberg given-names: Daniel orcid: "https://orcid.org/0000-0002-4012-5014" - email: denell@physik.hu-berlin.de family-names: Denell given-names: Thea orcid: "https://orcid.org/0009-0000-7185-9363" - email: andrea.albino@physik.hu-berlin.de family-names: Albino given-names: Andrea orcid: "https://orcid.org/0000-0001-9280-7431" - email: hampus.naesstroem@physik.hu-berlin.de family-names: Näsström given-names: Hampus orcid: "https://orcid.org/0000-0002-3264-1692" - email: sherjeel.shabih@physik.hu-berlin.de family-names: Shabih given-names: Sherjeel orcid: "https://orcid.org/0009-0008-6635-4465" - email: florian.dobener@physik.hu-berlin.de family-names: Dobener given-names: Florian orcid: "https://orcid.org/0000-0003-1987-6224" - email: markus.kuehbach@physik.hu-berlin.de family-names: Kühbach given-names: Markus orcid: "https://orcid.org/0000-0002-7117-5196" - email: mozumder@physik.hu-berlin.de family-names: Mozumder given-names: Rubel orcid: "https://orcid.org/0009-0007-5926-6646" - email: joseph.rudzinski@physik.hu-berlin.de family-names: Rudzinski given-names: Joseph F. orcid: "https://orcid.org/0000-0003-3403-640X" - email: ndaelman@physik.hu-berlin.de family-names: Daelman given-names: Nathan orcid: "https://orcid.org/0000-0002-7647-1816" - email: jose.pizarro@physik.hu-berlin.de family-names: Pizarro given-names: José M. orcid: "https://orcid.org/0000-0002-6751-8192" - email: kuban@physik.hu-berlin.de family-names: Kuban given-names: Martin orcid: "https://orcid.org/0000-0002-1619-2460" - email: cuauhtemoc.salazar@physik.hu-berlin.de family-names: Salazar given-names: Cuauhtemoc orcid: "https://orcid.org/0000-0002-9635-5062" - email: ondracka@mail.muni.cz family-names: Ondračka given-names: Pavel orcid: "https://orcid.org/0000-0003-0729-629X" - email: bungartz@cit.tum.de family-names: Bungartz given-names: Hans-Joachim orcid: "https://orcid.org/0000-0002-0171-0712" - email: claudia.draxl@physik.hu-berlin.de family-names: Draxl given-names: Claudia orcid: "https://orcid.org/0000-0003-3523-6657" contact: - email: markus.scheidgen@physik.hu-berlin.de family-names: Scheidgen given-names: Markus orcid: "https://orcid.org/0000-0002-8038-2277" doi: 10.5281/zenodo.8366163 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - email: markus.scheidgen@physik.hu-berlin.de family-names: Scheidgen given-names: Markus orcid: "https://orcid.org/0000-0002-8038-2277" - email: lauri.himanen@gmail.com family-names: Himanen given-names: Lauri orcid: "https://orcid.org/0000-0002-3130-8193" - email: alvin.noe.ladines@physik.hu-berlin.de family-names: Ladines given-names: Alvin Noe orcid: "https://orcid.org/0000-0003-0077-2097" - email: david.sikter@physik.hu-berlin.de family-names: Sikter given-names: David orcid: "https://orcid.org/0000-0002-2102-7160" - email: mohammad.nakhaee@physik.hu-berlin.de family-names: Nakhaee given-names: Mohammad orcid: "https://orcid.org/0000-0003-4146-0129" - email: adam@fekete.co.uk family-names: Fekete given-names: Ádám orcid: "https://orcid.org/0000-0002-6263-897X" - email: theodore.chang@physik.hu-berlin.de family-names: Chang given-names: Theodore orcid: "https://orcid.org/0000-0002-4911-0230" - email: amir.golparvar@physik.hu-berlin.de family-names: Golparvar given-names: Amir orcid: "https://orcid.org/0000-0002-2412-6615" - email: jose.marquez@physik.hu-berlin.de family-names: Márquez given-names: José A. orcid: "https://orcid.org/0000-0002-8173-2566" - email: sandor.brockhauser@physik.hu-berlin.de family-names: Brockhauser given-names: Sandor orcid: "https://orcid.org/0000-0002-9700-4803" - email: sebastian.brueckner@ikz-berlin.de family-names: Brückner given-names: Sebastian orcid: "https://orcid.org/0000-0002-5969-847X" - email: luca.ghiringhelli@physik.hu-berlin.de family-names: Ghiringhelli given-names: Luca M. orcid: "https://orcid.org/0000-0001-5099-3029" - email: felix.dietrich@tum.de family-names: Dietrich given-names: Felix orcid: "https://orcid.org/0000-0002-2906-1769" - email: d.lehmberg@tum.de family-names: Lehmberg given-names: Daniel orcid: "https://orcid.org/0000-0002-4012-5014" - email: denell@physik.hu-berlin.de family-names: Denell given-names: Thea orcid: "https://orcid.org/0009-0000-7185-9363" - email: andrea.albino@physik.hu-berlin.de family-names: Albino given-names: Andrea orcid: "https://orcid.org/0000-0001-9280-7431" - email: hampus.naesstroem@physik.hu-berlin.de family-names: Näsström given-names: Hampus orcid: "https://orcid.org/0000-0002-3264-1692" - email: sherjeel.shabih@physik.hu-berlin.de family-names: Shabih given-names: Sherjeel orcid: "https://orcid.org/0009-0008-6635-4465" - email: florian.dobener@physik.hu-berlin.de family-names: Dobener given-names: Florian orcid: "https://orcid.org/0000-0003-1987-6224" - email: markus.kuehbach@physik.hu-berlin.de family-names: Kühbach given-names: Markus orcid: "https://orcid.org/0000-0002-7117-5196" - email: mozumder@physik.hu-berlin.de family-names: Mozumder given-names: Rubel orcid: "https://orcid.org/0009-0007-5926-6646" - email: joseph.rudzinski@physik.hu-berlin.de family-names: Rudzinski given-names: Joseph F. orcid: "https://orcid.org/0000-0003-3403-640X" - email: ndaelman@physik.hu-berlin.de family-names: Daelman given-names: Nathan orcid: "https://orcid.org/0000-0002-7647-1816" - email: jose.pizarro@physik.hu-berlin.de family-names: Pizarro given-names: José M. orcid: "https://orcid.org/0000-0002-6751-8192" - email: kuban@physik.hu-berlin.de family-names: Kuban given-names: Martin orcid: "https://orcid.org/0000-0002-1619-2460" - email: cuauhtemoc.salazar@physik.hu-berlin.de family-names: Salazar given-names: Cuauhtemoc orcid: "https://orcid.org/0000-0002-9635-5062" - email: ondracka@mail.muni.cz family-names: Ondračka given-names: Pavel orcid: "https://orcid.org/0000-0003-0729-629X" - email: bungartz@cit.tum.de family-names: Bungartz given-names: Hans-Joachim orcid: "https://orcid.org/0000-0002-0171-0712" - email: claudia.draxl@physik.hu-berlin.de family-names: Draxl given-names: Claudia orcid: "https://orcid.org/0000-0003-3523-6657" date-published: 2023-10-15 doi: 10.21105/joss.05388 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 5388 title: "NOMAD: A distributed web-based platform for managing materials science research data" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05388" volume: 8 title: "NOMAD: A distributed web-based platform for managing materials science research data" ```

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editorialbot commented 9 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 9 months ago

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markus1978 commented 9 months ago

@zhubonan @Andrew-S-Rosen @sgbaird @berquist @Kevin-Mattheus-Moerman

I am very happy that the paper was accepted and published. Many thanks to all editors and reviewers.

Kevin-Mattheus-Moerman commented 9 months ago

@markus1978 congratulations on this publication in JOSS!

Thanks for editing @zhubonan!

And a special thank you to the reviewers: @arosen93, @berquist, @sgbaird

editorialbot commented 9 months ago

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zhubonan commented 9 months ago

Congrats @markus1978, and thanks to you all helping this work through the process! @berquist @Kevin-Mattheus-Moerman @Andrew-S-Rosen @sgbaird 🤝😆

Pepe-Marquez commented 9 months ago

Thank you very much to all the editors and reviewers! 🚀

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