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

[editorialbot]

Submitting author: @markus1978 (Markus Scheidgen)
Repository: https://github.com/nomad-coe/nomad
Branch with paper.md (empty if default branch): paper
Version: v1.1.8
Editor: @zhubonan
Reviewers: @arosen93, @berquist, @sgbaird
Managing EiC: Kevin M. Moerman

Status

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Markdown: [![status](https://joss.theoj.org/papers/5485aee97d291f2b545116d21c3b76c5/status.svg)](https://joss.theoj.org/papers/5485aee97d291f2b545116d21c3b76c5)

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@markus1978 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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[editorialbot]

Wordcount for paper.md is 1268

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1038/s41586-022-04501-x may be a valid DOI for title: FAIR data enabling new horizons for materials research
- 10.1063/1.4812323 may be a valid DOI for title: Commentary: The Materials Project: A materials genome approach to accelerating materials innovation
- 10.1007/s11837-013-0755-4 may be a valid DOI for title: Materials design and discovery with high-throughput density functional theory: the open quantum materials database (OQMD)
- 10.1038/s41524-018-0107-6 may be a valid DOI for title: Materials structure genealogy and high-throughput topological classification of surfaces and 2D materials
- 10.1016/j.commatsci.2012.10.028 may be a valid DOI for title: Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis
- 10.1557/mrs.2018.208 may be a valid DOI for title: NOMAD: The FAIR concept for big data-driven materials science
- 10.1038/s41524-017-0048-5 may be a valid DOI for title: Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats
- 10.1038/s41524-022-00935-z may be a valid DOI for title: The NOMAD Artificial-Intelligence Toolkit: turning materials-science data into knowledge and understanding

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@editorialbot set as branch

[editorialbot]

Done! branch is now

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=12.28 s (93.3 files/s, 190961.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                           179              3              0        1378027
XML                             27              8              0         611557
JavaScript                     438           6640          14546         179689
Python                         267          15691          23231          73121
CSS                             42             17            415          17366
Markdown                        42           2650              0           8764
YAML                           101            272            430           5494
TypeScript                       1              0              0           3036
SVG                             18              0              1            606
R                                1              5              0            586
Jupyter Notebook                 2              0            861            388
Bourne Shell                    19             93             45            251
PHP                              1            180              0            214
TOML                             1              8              0            151
Dockerfile                       1             52             52            127
HTML                             1             11             22             50
INI                              3              0              0             13
TeX                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                          1145          25630          39603        2279441
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[Kevin-Mattheus-Moerman]

@editorialbot set paper as branch

[editorialbot]

Done! branch is now paper

[Kevin-Mattheus-Moerman]

@markus1978 I am the AEiC on this track and here to help with the initial steps. For the moment, can you please work on the following:

• Can you address the those potentially missing DOIs? ☝️ You can call @editorialbot check references here to check them, and use @editorialbot generate pdf to update the paper if needed.
• Can you extend all affiliations to also have the city/town. Also you may want to include the department/discipline for each since some have it and some don't.

[Kevin-Mattheus-Moerman]

@editorialbot invite @chartgerink as editor

[editorialbot]

Invitation to edit this submission sent!

[zhubonan]

I just spoke with Kevin and I can actually handle this one. Hope that is OK with @chartgerink.

[zhubonan]

@editorialbot assign me as editor

[editorialbot]

Assigned! @zhubonan is now the editor

[markus1978]

@editorialbot check references

[editorialbot]

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
- 10.48550/arXiv.2205.14774 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

[markus1978]

@markus1978 I am the AEiC on this track and here to help with the initial steps. For the moment, can you please work on the following:

• Can you address the those potentially missing DOIs? ☝️ You can call @editorialbot check references here to check them, and use @editorialbot generate pdf to update the paper if needed.
• Can you extend all affiliations to also have the city/town. Also you may want to include the department/discipline for each since some have it and some don't.

@Kevin-Mattheus-Moerman thank you vera much for your comment and taking care of our contribution as a AEiC.

I added the DOIs and your bot seems to like my changes.

I also added the cities to all affiliations. Please note that some cities might appear twice: once because they belong to the name of the university, second as the city itself. I added the departments consistently in english where appropriate. Sebastian works as a data steward for the whole IKZ (affiliation 2) does not belong to a single department. The universities/institutes have their names according to their policies of using their names in english publications. I hope this is compatible with JOSS policies.

[zhubonan]

@editorialbot remove @pythonpanda2 from reviewers

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

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[zhubonan]

@editorialbot commands

[editorialbot]

Hello @zhubonan, here are the things you can ask me to do:

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[zhubonan]

@editorialbot remove @pythonpanda2 from reviewers

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[zhubonan]

@editorialbot list reviewers

[editorialbot]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[zhubonan]

@editorialbot remove @username from reviewers

[editorialbot]

@username is not in the reviewers list

[zhubonan]

@editorialbot remove @pythonpanda2 from reviewers

[editorialbot]

@pythonpanda2 removed from the reviewers list!

[zhubonan]

@editorialbot add @arosen93 as reviewer

[editorialbot]

@arosen93 added to the reviewers list!

[zhubonan]

Hello @sgbaird and @berquist this package seems to be in your area of expertise, would you be happy to help to review it?
You can find out more about JOSS here: https://joss.theoj.org/about

[berquist]

Yes, I would be happy to have this as my first review.

[sgbaird]

Hi all, I'm back from a long vacation, so I'm just now seeing this. It looks like you've found the reviewers that you need, but lmk if you need additional help. Great to see NOMAD getting some extra visibility this way!

[zhubonan]

Hi all, I'm back from a long vacation, so I'm just now seeing this. It looks like you've found the reviewers that you need, but lmk if you need additional help. Great to see NOMAD getting some extra visibility this way!

Thanks, good to have an extra pair of eyes as it is a quite a big package.

[zhubonan]

@editorialbot add @berquist as reviewer

[editorialbot]

@berquist added to the reviewers list!

[zhubonan]

@editorialbot add @sgbaird as reviewer

[editorialbot]

@sgbaird added to the reviewers list!

[zhubonan]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5388.