[PRE REVIEW]: Taming your metabolic datasets with MeDUSA

[editorialbot]

Submitting author: @laura-hetzel (Laura Ann Hetzel)
Repository: https://github.com/laura-hetzel/MeDUSA
Branch with paper.md (empty if default branch):
Version: v1.0
Editor: @jromanowska
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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Author instructions

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

@laura-hetzel 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.

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[editorialbot]

Checking the BibTeX entries failed with the following error:

No paper file path

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=1.49 s (42.4 files/s, 103731.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              9              1              0         114453
XML                              6              0              0          34900
R                               40            532           1417           2650
Markdown                         1             18              0             48
TeX                              1              6              0             48
Bourne Shell                     4             11             16             37
Dockerfile                       1              7             14             27
Python                           1              4              2             10
-------------------------------------------------------------------------------
SUM:                            63            579           1449         152173
-------------------------------------------------------------------------------

Commit count by author:

   114	Pascal
    72	NotEric
    26	Laura Hetzel
    14	Eman-Mu
    11	David Rasp
    10	klabla
     8	Merys Valdez
     8	Pascal Maas
     4	Ahmed Ali
     2	Alida Kindt-Dunjko
     1	StatisticsValdez

[editorialbot]

Paper file info:

⚠️ Failed to find a paper file in https://github.com/laura-hetzel/MeDUSA

[editorialbot]

⚠️ An error happened when generating the pdf. Paper file not found.

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[TheFollyLlama]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1002/anie.201709719 is OK
- 10.1038/nprot.2016.156 is OK
- 10.1021/ac051437y is OK
- 10.1093/nar/gkab382 is OK
- 10.1038/s41598-024-55356-3 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.3109/03014460.2013.807878. is INVALID

[TheFollyLlama]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.3109/03014460.2013.807878 is OK
- 10.1002/anie.201709719 is OK
- 10.1038/nprot.2016.156 is OK
- 10.1021/ac051437y is OK
- 10.1093/nar/gkab382 is OK
- 10.1038/s41598-024-55356-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@editorialbot invite @zhubonan as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@zhubonan this work may be somewhat outside of your usual domain, but I was wondering if you are familiar with the techniques employed and therefore able to handle it regardless. Thanks anyway.

[zhubonan]

@Kevin-Mattheus-Moerman Sorry, this is a bit far from my domain...

[Kevin-Mattheus-Moerman]

@editorialbot invite @diazrenata as editor

[editorialbot]

Invitation to edit this submission sent!

[diazrenata]

@editorialbot assign me as editor

[editorialbot]

Assigned! @diazrenata is now the editor

[diazrenata]

Hi @laura-hetzel! I'll be editing this submission. Have you had a chance to look at the reviewer application and identify any potential reviewers?

[TheFollyLlama]

Hi @diazrenata. Found a few: https://reviewers.joss.theoj.org/reviewers/search?language=29&area_id=&keywords=mass+spec

[diazrenata]

@editorialbot check repository

[Kevin-Mattheus-Moerman]

@diazrenata 👋

[ahmed-ali9]

Hi, would you like us to suggest reviewers as well? Maybe it can speed things a bit

[ahmed-ali9]

[email protected]

[Kevin-Mattheus-Moerman]

@ahmed-ali9 apologies for the delays encountered here. The handling editor is resigning and hence was not responding here. I'll assign myself for the moment so I can keep a close eye on this issue. I'll either find reviewers myself or will assign an alternative editor shortly.

[Kevin-Mattheus-Moerman]

@editorialbot assign me as editor

[editorialbot]

Assigned! @Kevin-Mattheus-Moerman is now the editor

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@jromanowska do you think you can take over this one from me as editor?

[jromanowska]

Yes, I can! :)

[jromanowska]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[jromanowska]

Hi, @laura-hetzel 👋
I will take care of the process from now on. I will try to find reviewers, but first I need some clarifications from you. You indicated that @ahmed-ali9 is the corresponding author, but he did not make any contributions to the repository. Please explain how did he contribute to the work (as you can read in the Documentation, purely organizational or financial contributions is not enough for co-authorship in JOSS paper).

Moreover, by "corresponding author", we mean the one who can handle any questions about the implementations, comments from the reviewers, etc. Usually, it's the author who also contributed most to the development of the software.

Last, but not least, could you comment on the licence choice? It's not a standard choice for scientific software.

Oh, and one more, minor thing: could you explain the title to me?

[laura-hetzel]

Hi @jromanowska ,
First of all, very excited this is gaining traction again!
@ahmed-ali9 is heavily involved in the conceptualization of this project, and he will continue to build on it with other students. Some of the new developments are currently in progress. Also, the logic behind the functions and data processing was developed by him. I will be finishing my PhD soon (yay!) and this project will be passed on, however, Ahmed will remain the point of contact and have the overview of any updates.
The license was recommended by our IT department, so we accepted it as it complies with what we want for the project as well as what the university requires.
As for the title, direct infusion is a method of mass spectrometry, and this software was developed specifically for this mehtod. Most software in our field is developed for a different method and is therefore not useful to us, so we thought it was important to include "direct infusion" in the title. MeDUSA stands for MEtabolomics for Direct-infusion Untargeted Single-cell Analysis and this captures all of the important concepts that sets the software apart from anything else currently available.

[jromanowska]

Thank you for the clarifications, @laura-hetzel. Wishing you luck with wrapping up your PhD - it always seems far too much to do in the last months, but you'll make it!

The conceptualization is enough to be on the author list, but I still think that since it was you who implemented that, you should be the corresponding author on this submission.

I will have to ask the other editors about the license, but I think it's fine.

Thanks for the clarification of "direct infusion" - I was wondering more about the "staring down" phrase... I'm not a native English speaker and I didn't really catch the meaning of this title. (I'm sure it's fine, I just wanted to be able to understand that 😅 )

And one more thing - do you have a non-cis-male candidate for a reviewer?

[Kevin-Mattheus-Moerman]

@jromanowska the license artistic-2.0 seems okay. It is the first time I see this one but it does seem to be an OSI approved license and therefore acceptable: https://opensource.org/license/artistic-2-0.

I recommend that the authors list, link to, and name the license in their README if they don't already (and even to create a license badge for it for clarity). Also they should check whether the license text is unaltered. It should be exactly like the text from the link. I say this because this may be why GitHub lists it as Other at the moment.

[ahmed-ali9]

Thank you for the clarifications, @laura-hetzel. Wishing you luck with wrapping up your PhD - it always seems far too much to do in the last months, but you'll make it!

The conceptualization is enough to be on the author list, but I still think that since it was you who implemented that, you should be the corresponding author on this submission.

I will have to ask the other editors about the license, but I think it's fine.

Thanks for the clarification of "direct infusion" - I was wondering more about the "staring down" phrase... I'm not a native English speaker and I didn't really catch the meaning of this title. (I'm sure it's fine, I just wanted to be able to understand that 😅 )

And one more thing - do you have a non-cis-male candidate for a reviewer?

Hi @jromanowska ,
I do not mind not being corresponding author for this (especially that laura needs to graduate, so avoiding delays is the name of the game now).
Please keep in mind that as she stated, she is moving on to brighter pastures after this, so she will likely not be able to respond in a timely manner to requests. Since i was involved from the beginning and i'm continuing this project as well, thats why we opted to put me as corresponding author.

Perhaps we can both be co-corresponding authors?
If its not possible, i'm happy with laura being corresponding author.

Regarding the reviewer, I can suggest the following:
[email protected]. ; https://laurazwep.com/
Dr. Marina Meester ; https://www.uu.nl/staff/MMeester
Prof. BERNASCONI ANNA ;https://www.deib.polimi.it/eng/people/details/711462

Thanks!

[jromanowska]

Thank you, @ahmed-ali9. Now all is clear! 🙌 I will, then refer to both of you when writing to authors.

And thank you for the reviewer suggestions!

(I'd really appreciate explanation of the title, as I mentioned above)

[ahmed-ali9]

Thank you, @ahmed-ali9. Now all is clear! 🙌 I will, then refer to both of you when writing to authors.

And thank you for the reviewer suggestions!

(I'd really appreciate explanation of the title, as I mentioned above)

Hi!
Staring down can be thought of as "conquering" or "dealing with". I hope this helps :)

[jromanowska]

I've found this definition and it might be that in this light your title is not the best: https://dictionary.cambridge.org/dictionary/english/stare-down ... (I'm just trying to wrap my head around it - just thinking that it would be difficult to find a reviewer if the title is not understood well)...

[laura-hetzel]

In an effort to not get stuck on the title, we propose changing the title to "Taming your metabolic datasets with MeDUSA". @jromanowska if you find this more suitable, I will change it in the pdf on github.

[jromanowska]

Thank you, @laura-hetzel - this sounds great! I will change the title of the issue.

[jromanowska]

👋 @sunbrn, @waxlamp, @ByrumLab & @joannawolthuis, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html