[REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction

[editorialbot]

Submitting author: @htwangtw (Hao-Ting Wang)
Repository: https://github.com/bids-apps/giga_connectome
Branch with paper.md (empty if default branch):
Version: 0.5.0
Editor: @mstimberg
Reviewers: @jdkent, @shnizzedy, @emullier
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/9edfa53b0ee4d33931cff3b5429e9c27/status.svg)](https://joss.theoj.org/papers/9edfa53b0ee4d33931cff3b5429e9c27)

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

@jdkent & @shnizzedy, 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 @mstimberg 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 @jdkent

📝 Checklist for @shnizzedy

📝 Checklist for @emullier

[editorialbot]

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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]

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

OK DOIs

- 10.5281/zenodo.8397156 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1011942 is OK
- 10.1038/s41592-022-01681-2 is OK
- 10.1016/j.schres.2005.11.020 is OK
- 10.1016/j.biopsych.2006.06.027 is OK
- 10.1176/appi.ajp.162.7.1256 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1093/cercor/bhx179 is OK
- 10.12688/mniopenres.12767.2 is OK
- 10.1016/j.neuroimage.2020.117126 is OK
- 10.17605/OSF.IO/T7JKZ is OK
- 10.1002/hbm.25829 is OK
- 10.1101/2021.12.01.470790 is OK
- 10.1089/brain.2012.0073 is OK
- 10.1101/2023.11.20.567926 is OK
- 10.1038/mp.2013.78 is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.3389/fnsys.2012.00062 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1816.7 files/s, 128850.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            375            415           1612
Markdown                        10            261              0            737
YAML                            11             41             38            444
TeX                              1             21              0            262
JSON                            16              0              0            178
TOML                             1             13              3            117
INI                              1              3              6             36
reStructuredText                 2             20             29             29
DOS Batch                        1              8              1             26
Jinja Template                   1              7              0             21
Dockerfile                       1              9              1             15
make                             1              4              7              9
SVG                              1              0              1              3
-------------------------------------------------------------------------------
SUM:                            67            762            501           3489
-------------------------------------------------------------------------------

Commit count by author:

    69	Hao-Ting Wang
    55	Remi Gau
    11	dependabot[bot]
     7	htwangtw
     3	pre-commit-ci[bot]
     2	github-actions[bot]
     1	Quentin Dessain

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1068

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[mstimberg]

👋🏼 @htwangtw, @jdkent, @shnizzedy this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

at the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please feel free to ping me (@mstimberg) if you have any questions/concerns.

[shnizzedy]

Review checklist for @shnizzedy

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review. ([REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061 (comment), [REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061 (comment), [REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061 (comment))

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/bids-apps/giga_connectome?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@htwangtw) made major contributions to the software? Does the full list of paper authors seem appropriate and complete? (Document contributors and their roles bids-apps/giga_connectome#161)
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed? (UnboundLocalError: local variable 'connectome_path' referenced before assignment bids-apps/giga_connectome#164)
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). (Add examples bids-apps/giga_connectome#166)
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to
  • 1) Contribute to the software
  • 2) Report issues or problems with the software
  • 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[jdkent]

Review checklist for @jdkent

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/bids-apps/giga_connectome?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@htwangtw) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[shnizzedy]

@mstimberg I was unaware of this work prior to being invited to review. I think I am able to make an impartial assessment of this work and request that these conflicts be waived:

Conflicts of interest

• Rémi Gau and I are co-authors (4th and 11th, respectively, of 19 co-authors) on a currently-in-review paper¹ describing a metadata project² that we both contributed to.
• Rémi Gau, Pierre Bellec and I were all involved in getting the NMIND Consortium^3,4 (devising best practices to improve reproducibility and reduce duplicated effort) off the ground.
• Rémi Gau and Pierre Bellec have both published papers^5,6 describing Brainhack, a recurring workshop with a New York City event hosted annually by my employer, the Child Mind Institute. All of the authors and myself are members of the Brainhack community with profiles on the Brainhack Mattermost⁷.
• I'm a co-author of a pre-print⁸ cited in this manuscript⁹.

References

Footnotes

1. Chen Y, Jarecka D, Abraham SA, Gau R, Ng E, Low DM, Bevers I, Johnson A, Keshavan A, Klein A, Clucas J, Rosli Z, Hodge SM, Linkersdörfer J, Bartsch H, Das S, Fair D, Kennedy D, Ghosh SS. (2024). ReproSchema: Enhancing Research Reproducibility through Standardized Survey Data Collection. JMIR Preprints. 21/06/2024:63343. DOI:10.2196/preprints.63343. ↩

2. Reproschema Contributors. (2020). ReproNim/reproschema: 1.0.0 Release Candidate 2 (1.0.0-rc2). Zenodo. DOI:10.5281/zenodo.4064940. ↩

3. NMIND. ↩

4. Kiar G, Clucas J, Feczko E, et al. (2023). Align with the NMIND consortium for better neuroimaging. Nat Hum Behav 7, 1027–1028. DOI:10.1038/s41562-023-01647-0. ↩

5. Gau R, Noble S, Heuer K, et al. (2021). Brainhack: Developing a culture of open, inclusive, community-driven neuroscience. Neuroview 109, 11, 1769-1775. DOI:10.1016/j.neuron.2021.04.001. ↩

6. Craddock RC, Margulies DS, Bellec P, et al. (2016). Brainhack: a collaborative workshop for the open neuroscience community. GigaScience 5, 1. DOI:10.1186/s13742-016-0121-x. ↩

7. Brainhack Mattermost.
   
   
   ↩

8. Li X, Esper NB, Ai L, Giavasis S, Jin H, Feczko E, Xu T, Clucas J, et al. (2024). Moving Beyond Processing and Analysis-Related Variation in Neuroscience. bioRxiv 2021.12.01.470790. DOI:10.1101/2021.12.01.470790. ↩

9. BibTeX entry cited on line 62 in Giga Connectome: a BIDS-app for time series and functional connectome extraction. ↩

[mstimberg]

@shnizzedy Many thanks for the detailed information. From my side, I'd say that the last point is not an issue (it regularly happens that reviewers are authors of software in the same field that get cited by the reviewed manuscript). I am also not worried about all of you being part of the Brainhack community – reviewers and authors being part of the same community is difficult to avoid if we want to have competent reviewers 😊
The first two points are less clear, but again, I'd waive that COI. From what I see, a lot of people in the field are in some way part of the BIDS community, so these kinds of interactions seem to be hard to avoid. However, I'd be more comfortable if the track editor signed off on this as well. @Kevin-Mattheus-Moerman, what do you think?

CC @sappelhoff who is both a JOSS editor and a BIDS maintainer, so he might have valuable insights to add.

[sappelhoff]

From what I see, a lot of people in the field are in some way part of the BIDS community, so these kinds of interactions seem to be hard to avoid.

I agree ✅

I believe the COI for @shnizzedy can be waived.

[mstimberg]

@editorialbot add @emullier as reviewer

Thanks for joining us!

[editorialbot]

@emullier added to the reviewers list!

[emullier]

Review checklist for @emullier

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/bids-apps/giga_connectome?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@htwangtw) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?