[REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061

editorialbot · 2024-07-30T16:05:59Z

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, @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

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-07-30T16:06:03Z

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editorialbot · 2024-07-30T16:06:17Z

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 · 2024-07-30T16:06:19Z

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 · 2024-07-30T16:06:24Z

Paper file info:

📄 Wordcount for paper.md is 1068

✅ The paper includes a Statement of need section

editorialbot · 2024-07-30T16:06:26Z

License info:

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

editorialbot · 2024-07-30T16:07:55Z

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

mstimberg · 2024-07-30T16:08:31Z

👋🏼 @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 · 2024-07-30T16:50:03Z

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))
[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 · 2024-07-30T18:35:37Z

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 · 2024-08-01T14:36:22Z

@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 Consortium³^,⁴ (devising best practices to improve reproducibility and reduce duplicated effort) off the ground.
Rémi Gau and Pierre Bellec have both published papers⁵^,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

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

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

mstimberg · 2024-08-01T16:23:02Z

@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 · 2024-08-01T17:27:13Z

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 · 2024-08-06T16:34:48Z

@editorialbot add @emullier as reviewer

Thanks for joining us!

editorialbot · 2024-08-06T16:34:51Z

@emullier added to the reviewers list!

emullier · 2024-08-27T06:47:55Z

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?

mstimberg · 2024-09-02T12:28:18Z

Hi @jdkent and @emullier, did you already have a chance to have a closer look at the software and paper?

Please be reminded of our review recommendations:

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.)

@htwangtw: please have another look at the issues opened by @shnizzedy and update their status (e.g. close them) if necessary 🙏

emullier · 2024-09-03T10:57:30Z

Hi @mstimberg, I started to play with the software 2 days ago, I currently have some issues running it on my subject
I opened two issues about my problems in running it on my subject (issue bids-apps/giga_connectome#171 and issue bids-apps/giga_connectome#172).
Maybe if I could have some feedback on this?

htwangtw · 2024-09-03T14:31:12Z

Hi @jdkent and @emullier, did you already have a chance to have a closer look at the software and paper?

Please be reminded of our review recommendations:

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.)

@htwangtw: please have another look at the issues opened by @shnizzedy and update their status (e.g. close them) if necessary 🙏

Thanks for the reminder - I will get back on to this soon!

Kevin-Mattheus-Moerman · 2024-09-05T10:50:49Z

@mstimberg I think it would be best to remove @shnizzedy as a reviewer. There does seem to be either a potential or perceived COI, especially relating to the shared authorship and consortium membership which show a prolonged collaboration.

@shnizzedy thanks for sharing this information, and thanks for offering to help. Unfortunately our policies are quite strict on potential/perceived COIs. Hence we will proceed to remove you as reviewer. We do hope we may ask for your assistance for a different JOSS submission in the future. Thanks agian.

mstimberg · 2024-09-05T12:34:57Z

Dear @shnizzedy, apologies that this took so long, and even more apologies that the final decision is contrary to what I indicated earlier. As @Kevin-Mattheus-Moerman explained above, we finally consider your closeness to some of the authors as being a potential COI – or at least perceivable as one. I therefore regret that I'll have to officially remove you as a reviewer. Thanks a million for your involvement, though, and I'd be very happy to see you come back to JOSS as a reviewer (or author) another time.

@htwangtw Of course, this does not mean that you have to discard the issues opened by @shnizzedy, please feel free to address them as you see fit.

mstimberg · 2024-09-05T12:35:10Z

@editorialbot remove @shnizzedy from reviewers

editorialbot · 2024-09-05T12:35:12Z

@shnizzedy removed from the reviewers list!

mstimberg · 2024-09-26T08:21:04Z

👋 @emullier did you find time to have another look at the software? Please note that the authors have replied in the two issues you opened (bids-apps/giga_connectome#171 and bids-apps/giga_connectome#171).

@jdkent Can you please give us an estimate when you will be able to review this submission?

mstimberg · 2024-10-15T13:26:16Z

@emullier & @jdkent, could you please give us an update ?

👋 @emullier did you find time to have another look at the software? Please note that the authors have replied in the two issues you opened (bids-apps/giga_connectome#171 and bids-apps/giga_connectome#171).

@jdkent Can you please give us an estimate when you will be able to review this submission?

htwangtw · 2024-10-15T15:00:14Z

I will try to look for any potential blockers this week. Really sorry for the delay on my side too

jdkent · 2024-11-25T14:29:20Z

apologies on my long delay, I am walking through the code and documentation now and will be done by the end of this week.

jdkent · 2024-12-02T13:16:07Z

I have a few nitpicks as issues in the repository, but I do not see those as a reason to hold back the publication of this software in JOSS.

mstimberg · 2024-12-02T13:24:43Z

Many thanks for your review, @jdkent. Just for reference, here the links to the issues you opened: bids-apps/giga_connectome#184, bids-apps/giga_connectome#185, bids-apps/giga_connectome#186

As you said, these do not seem to be major issues, but I'd suggest that the authors have a look at them and see whether they can be addressed easily.

mstimberg · 2025-01-30T17:12:29Z

👋 Hi and a belated Happy New Year (or a not so belated Chinese New Year for all those who celebrate) 🎆 !

@emullier could you please give us an update:

👋 @emullier did you find time to have another look at the software? Please note that the authors have replied in the two issues you opened (bids-apps/giga_connectome#171 and bids-apps/giga_connectome#171).

@jdkent I think that @htwangtw addressed the issues that you opened, could you please have a look whether these solutions/answers work for you and update your checklist if necessary?

Thanks 🙏 !

htwangtw · 2025-01-30T17:35:51Z

Thank you for following up @mstimberg

I am going to have some further updates as some of the issues opened by @emullier can be addressed with improved documentation.

Thank you all for the patience!

editorialbot added Jinja Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jul 30, 2024

editorialbot assigned mstimberg Jul 30, 2024

editorialbot mentioned this issue Jul 30, 2024

[PRE REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #6630

Closed

shnizzedy mentioned this issue Jul 31, 2024

Document contributors and their roles bids-apps/giga_connectome#161

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shnizzedy mentioned this issue Aug 9, 2024

Add examples bids-apps/giga_connectome#166

Open

emullier mentioned this issue Sep 3, 2024

Unclear inputs required bids-apps/giga_connectome#171

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[REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061

[REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061

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[REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061

[REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #7061

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mstimberg commented Jan 30, 2025

htwangtw commented Jan 30, 2025

editorialbot commented Jul 30, 2024 •

edited

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shnizzedy commented Jul 30, 2024 •

edited

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jdkent commented Jul 30, 2024 •

edited

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emullier commented Aug 27, 2024 •

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emullier commented Sep 3, 2024 •

edited by mstimberg

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mstimberg commented Sep 26, 2024 •

edited

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