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

Open editorialbot opened 3 months ago

editorialbot commented 3 months ago

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

Status

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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 commented 3 months ago

Hello humans, 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 commented 3 months ago 
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 commented 3 months ago

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 commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1068

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

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

editorialbot commented 3 months ago

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

mstimberg commented 3 months ago

👋🏼 @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 commented 3 months ago

Review checklist for @shnizzedy

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jdkent commented 3 months ago

Review checklist for @jdkent

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

shnizzedy commented 3 months ago

@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

References

[^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.

[^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.
Hao-Ting Wang Rémi Gau Natasha Clarke Quentin Dessain Pierre Bellec Jon Clucas [^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 commented 3 months ago

@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 :blush: 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 commented 3 months ago

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 commented 3 months ago

@editorialbot add @emullier as reviewer

Thanks for joining us!

editorialbot commented 3 months ago

@emullier added to the reviewers list!

emullier commented 2 months ago

Review checklist for @emullier

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mstimberg commented 2 months ago

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 :pray:

emullier commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

@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 commented 2 months ago

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 commented 2 months ago

@editorialbot remove @shnizzedy from reviewers

editorialbot commented 2 months ago

@shnizzedy removed from the reviewers list!

mstimberg commented 1 month ago

:wave: @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 commented 1 month ago

@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 commented 1 month ago

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