[PRE REVIEW]: lys: interactive multi-dimensional data analysis and visualization platform

[editorialbot]

Submitting author: !--author-handle-->@lys-devel<!--end-author-handle-- (Asuka Nakamura) Repository: https://github.com/lys-devel/lys Branch with paper.md (empty if default branch): review Version: v0.3.2 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @kuadrat, @ziatdinovmax, @pr4deepr Managing EiC: Daniel S. Katz

Status

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Markdown: [![status](https://joss.theoj.org/papers/f6eb85c0c03099f7ec91db24ffcef3e1/status.svg)](https://joss.theoj.org/papers/f6eb85c0c03099f7ec91db24ffcef3e1)

Author instructions

Thanks for submitting your paper to JOSS @lys-devel. Currently, there isn't a JOSS editor assigned to your paper.

@lys-devel if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

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

For a list of things I can do to help you, just type:

@editorialbot commands

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.82 s (553.9 files/s, 156429.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           200           9160            600          57612
Python                         154           5336           4225          18475
JavaScript                      16           4511           4394          16122
SVG                              1              0              0           2671
reStructuredText                67            764            646           1000
CSS                              4            187             35            756
Markdown                         6            167              0            648
TeX                              1             16              0            202
DOS Batch                        1             23              1            166
make                             1             24              5            124
Bourne Shell                     1              8              3             34
YAML                             1              1              4             21
-------------------------------------------------------------------------------
SUM:                           453          20197           9913          97831
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1290

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK

MISSING DOIs

- 10.25080/majora-7b98e3ed-013 may be a valid DOI for title: Dask: Parallel computation with blocked algorithms and task scheduling
- 10.1109/mcse.2011.35 may be a valid DOI for title: Mayavi: 3D Visualization of Scientific Data

INVALID DOIs

- None

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

👋 @lys-devel - Thanks for your submission, nut note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. In this case, it points out that Author (Asuka Nakamura) is missing affiliation. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[lys-devel]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK

MISSING DOIs

- None

INVALID DOIs

- None

[lys-devel]

@editorialbot generate pdf

[editorialbot]

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

[lys-devel]

@danielskatz Thank you for the quick reply. I fixed the references and affiliation and confirm the article proof.

[danielskatz]

👋 @emdupre - do you think you could edit this submission?

[danielskatz]

@editorialbot invite @emdupre as editor

[editorialbot]

Invitation to edit this submission sent!

[emdupre]

Hi @danielskatz, happy to take this ! Thanks for the invitation.

[emdupre]

@editorialbot assign @emdupre as editor

[editorialbot]

Assigned! @emdupre is now the editor

[emdupre]

👋 Hi @lys-devel, and thanks for your submission to JOSS !

If you have suggestions for potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here.

You can suggest reviewers from any relevant project, though we often recommend starting with this database of people who have already agreed to review for JOSS.

I'll put together a list of folks to reach out to as reviewers based on these suggestions and my own recommendations. I'll update this thread with that outreach.

[lys-devel]

Hi @emdupre, thank you for the editorial effort. I suggest potential reviewers who may be interested in the reviewing my software.

• dxm447
• jonatanalvelid
• kuadrat

[emdupre]

👋 Hi @jonatanalvelid, @kasasxav, @kuadrat,

Would you be willing to review lys: interactive multi-dimensional data analysis and visualization platform for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.05802/joss.05802/10.21105.joss.05802.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

[kuadrat]

Dear @emdupre , I would be happy to review this exciting submission!

However, I am the developer of data-slicer, a 3D data visualization and analysis tool. On quick inspection, data-slicer appears to have significant overlap with lys, both in functionality and targeted use-case.

I didn't find any mention of this being a problem in terms of conflict of interest or similar in the reviewing guideline. Nevertheless, I thought I'd disclose it here and ask you for confirmation that this does not disqualify me from reviewing lys.

[emdupre]

Thank you for your enthusiastic response, @kuadrat !

We do not consider it as a conflict-of-interest to work on a related project, provided there is no co-development ; rather, this is likely to bring especially valuable perspective to your review.

That being said, if you feel that you cannot provide an impartial review because of your work on data-slicer (e.g., because you feel that the two projects are in competition), then this would likely constitute a conflict-of-interest. Please let me know what you think, and thank you again !

[kuadrat]

Thanks for your response, @emdupre .

I personally believe that I am able to review this project impartially.

1. The goal in developing data-slicer was to make the lives of fellow scientists easier. In that sense, if a tool comes along that better accomplishes what data-slicer could also be used for, that's completely in the spirit of data-slicer, even if it itself becomes redundant. As you stated, I'd be happy to bring in my experience and perspective to lys.
2. Realistically speaking, I don't have any resources to continue development and maintenance of data-slicer. Therefore, I would be happy to see an actively maintained alternative becoming available.

Despite this, I imagine that it could be perceived by others (maybe even the author, @lys-devel ) that the projects are competing and I would therefore make a bad choice of referee. Still, even in this case and given that papers in JOSS aren't typically rejected but instead the referee's are asked to make concrete suggestions for improvement, it seems to me that I should be eligible to review this. I would like to leave the final call to you, though.

[emdupre]

Thank you for your thoughtful perspective, @kuadrat !

Given your described position, I believe that your work on data-slicer would not be a clear conflict of interest, and that lys would significantly benefit from your review.

I'll plan to add you as a reviewer with this in mind. If you have any remaining concerns, of course, please let me know !

[emdupre]

@editorialbot add @kuadrat as reviewer

[editorialbot]

@kuadrat added to the reviewers list!

[emdupre]

👋 Hi @ThFriedrich @pr4deepr @ziatdinovmax,

Would you be willing to review lys: interactive multi-dimensional data analysis and visualization platform for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.05802/joss.05802/10.21105.joss.05802.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

[ziatdinovmax]

Will be happy to review it!

On Fri, Sep 22, 2023 at 12:44 PM Elizabeth DuPre @.***> wrote:

👋 Hi @ThFriedrich https://github.com/ThFriedrich @pr4deepr https://github.com/pr4deepr @ziatdinovmax https://github.com/ziatdinovmax,

Would you be willing to review lys: interactive multi-dimensional data analysis and visualization platform for JOSS (the Journal of Open Source Software) https://joss.theoj.org/?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

The review takes place on GitHub and focuses on the software https://github.com/lys-devel/lys and this short paper:

https://github.com/openjournals/joss-papers/blob/joss.05802/joss.05802/10.21105.joss.05802.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5802#issuecomment-1731729112, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIFIU24GMBJXSU2Z4ELAL43X3W57VANCNFSM6AAAAAA4IROUDE . You are receiving this because you were mentioned.Message ID: @.***>

-- "Intelligence is the ability to adapt to change." - Stephen Hawking.

[emdupre]

Thank you, @ziatdinovmax ! I'll go ahead and add you as a reviewer now.

I'll give a bit longer to confirm if @jonatanalvelid, @kasasxav, @ThFriedrich, or @pr4deepr would be available as a third reviewer before moving forward 🚀

[emdupre]

@editorialbot add @ziatdinovmax as reviewer

[editorialbot]

@ziatdinovmax added to the reviewers list!

[pr4deepr]

Hi @emdupre

Happy to review this.

Cheers

Pradeep

[emdupre]

Thank you, @pr4deepr ! I'll go ahead and add you as a reviewer now 🚀

@jonatanalvelid, @kasasxav, @ThFriedrich, we now have enough reviewers to proceed, so I'll go ahead and move forward with starting the review process for lys. Thank you, though, for your consideration ! 🌻

[emdupre]

@editorialbot add @pr4deepr as reviewer

[editorialbot]

@pr4deepr added to the reviewers list!

[emdupre]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5869.