[PRE REVIEW]: The Neuroimaging Data Model (NIDM) Linear Regression Tool

[whedon]

Submitting author: @AKUMAR0019 (Ashmita Kumar) Repository: https://github.com/AKUMAR0019/PyNIDM Version: v.3.8.2 Editor: @osorensen Reviewers: @htwangtw, @robbisg Managing EiC: Kevin M. Moerman

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Status

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Author instructions

Thanks for submitting your paper to JOSS @AKUMAR0019. Currently, there isn't an JOSS editor assigned to your paper.

@AKUMAR0019 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

@whedon commands

[whedon]

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1611

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.23 s (485.6 files/s, 156703.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          75           2759           4099          10589
JavaScript                       8           2166           2178           8618
CSS                              4            323             42           1026
reStructuredText                 3            416            672            992
HTML                             3            340              6            543
TeX                              1             21              0            389
YAML                             4              8              2            349
Markdown                         6             41              0            115
DOS Batch                        1              8              1             27
Dockerfile                       1             12              0             26
Bourne Shell                     4              4             17             10
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           111           6102           7023          22694
-------------------------------------------------------------------------------

Statistical information for the repository 'eda0f32c87ed35d77a7a9abd' was
gathered on 2021/08/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
AKUMAR0019                      52          5086           3571           15.10
Al                               2           326             39            0.64
Al Crowely                       2           451            144            1.04
Al Crowley                      27          4134            958            8.88
Ashmita Kumar                   16          1615            329            3.39
David Keator                   295         28591           7923           63.69
Dorota Jarecka                  25           436            971            2.45
Michael Hanke                    1            19             12            0.05
Nazek Queder                     1             1              1            0.00
Sanu Ann                         6          2380            113            4.35
Satrajit Ghosh                   5            75             23            0.17
Tom Gillespie                    1             2              1            0.01
Tristan Glatard                  5            65              7            0.13
dorota                           1             4              3            0.01
maxbachmann                      1             2              2            0.01
natachaperez                     1            45              2            0.08
tiborauer                        1             2              2            0.01

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
AKUMAR0019                 3082           60.6          1.5                6.91
Al                           94           28.8         20.9                1.06
Al Crowley                 3661           88.6         15.5                7.27
David Keator              20815           72.8         31.7               20.12
Dorota Jarecka              346           79.4         44.7               12.72
Sanu Ann                   2297           96.5         38.0               10.19
Satrajit Ghosh               54           72.0         43.5               11.11
Tristan Glatard              26           40.0         45.3               23.08
dorota                        4          100.0         35.4               25.00
tiborauer                     2          100.0         23.1                0.00

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1038/sdata.2016.102 may be a valid DOI for title: Sharing brain mapping statistical results with the neuroimaging data model
- 10.1016/j.neuroimage.2013.05.094 may be a valid DOI for title: Towards structured sharing of raw and derived neuroimaging data across existing resources

INVALID DOIs

- None

[whedon]

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

[Kevin-Mattheus-Moerman]

@AKUMAR0019 Thanks for this submission to JOSS. I will be reviewing this work for scope and will look for a handling editor. In the mean time can you check those DOI's :point_up:.

You can call the following to update the paper: whedon generate pdf

[Kevin-Mattheus-Moerman]

@emdupre this looks like something you might be able to handle but I have waitlisted this submission for now since you seem to be at capacity in terms of handling submission. Let me know if once you available this is something you could help with. Thanks.

[whedon]

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

[AKUMAR0019]

@AKUMAR0019 Thanks for this submission to JOSS. I will be reviewing this work for scope and will look for a handling editor. In the mean time can you check those DOI's ☝️.

You can call the following to update the paper: whedon generate pdf

Thank you so much! Those DOIs were correct, and I will have whedon update the paper.

[AKUMAR0019]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[AKUMAR0019]

@whedon check references

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1038/sdata.2016.102 may be a valid DOI for title: Sharing brain mapping statistical results with the neuroimaging data model
- 10.1016/j.neuroimage.2013.05.094 may be a valid DOI for title: Towards structured sharing of raw and derived neuroimaging data across existing resources

INVALID DOIs

- None

[AKUMAR0019]

@whedon check references

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1038/sdata.2016.102 may be a valid DOI for title: Sharing brain mapping statistical results with the neuroimaging data model
- 10.1016/j.neuroimage.2013.05.094 may be a valid DOI for title: Towards structured sharing of raw and derived neuroimaging data across existing resources

INVALID DOIs

- None

[AKUMAR0019]

@whedon check references

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1038/sdata.2016.102 may be a valid DOI for title: Sharing brain mapping statistical results with the neuroimaging data model
- 10.1016/j.neuroimage.2013.05.094 may be a valid DOI for title: Towards structured sharing of raw and derived neuroimaging data across existing resources

INVALID DOIs

- None

[AKUMAR0019]

@whedon check references

[whedon]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "month" (NAME) [#, "@", #, {:title=>["Towards structured sharing of raw and derived neuroimaging data across existing resources"], :author=>["Keator, D B and Helmer, K and Steffener, J and Turner, J A and Van Erp, T G M and Gadde, S and Ashish, N and Burns, G A and Nichols, B N"], :abstract=>["Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery."], :journal=>["Neuroimage"], :volume=>"82", :pages=>["647--661"], :doi=>["{10.1016/j.neuroimage.2013.05.094}"]}]

[AKUMAR0019]

@whedon check references

[whedon]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "month" (NAME) [#, "@", #, {:title=>["Towards structured sharing of raw and derived neuroimaging data across existing resources"], :author=>["Keator, D B and Helmer, K and Steffener, J and Turner, J A and Van Erp, T G M and Gadde, S and Ashish, N and Burns, G A and Nichols, B N"], :abstract=>["Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery."], :journal=>["Neuroimage"], :volume=>"82", :pages=>["647--661"], :doi=>["10.1016/j.neuroimage.2013.05.094"]}]

[AKUMAR0019]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/sdata.2016.102 is OK
- 10.1016/j.neuroimage.2013.05.094 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[AKUMAR0019]

@whedon generate pdf

[whedon]

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

[AKUMAR0019]

I'm sorry for all of the comments! I wasn't sure how to test the paper, so I used whedon.

[emdupre]

@emdupre this looks like something you might be able to handle but I have waitlisted this submission for now since you seem to be at capacity in terms of handling submission. Let me know if once you available this is something you could help with. Thanks.

Thanks for the thought, @Kevin-Mattheus-Moerman ! I am at capacity right now but would be happy to take this on as things move off my docket in the next few weeks. I'll flag, though, that I work directly with one of the co-authors (Poline) and so have a COI on this submission. Let me know how you'd like to proceed !

[emdupre]

I'm sorry for all of the comments! I wasn't sure how to test the paper, so I used whedon.

Just to note that there's a Whedon preview service, if you haven't seen it already ! https://whedon.theoj.org

[Kevin-Mattheus-Moerman]

@emdupre Thanks. However, my apologies but given your perceived COI I will have to look for a different editor for this.

[Kevin-Mattheus-Moerman]

@fabian-s is this something your could help edit?

[Kevin-Mattheus-Moerman]

@whedon invite @fabian-s as editor

[whedon]

@fabian-s has been invited to edit this submission.

[fabian-s]

Sorry, I'd rather not -- I don't know Python, I don't do Neuroimaging.

[osorensen]

@Kevin-Mattheus-Moerman, I'd be happy to edit this submission.

[danielskatz]

@osorensen - feel free to assign this to yourself, using @whedon assign me as editor (and feel free to do this going forward when you see something that is of interest to you, as long as it's not undergoing scope review)

[osorensen]

@whedon assign @osorensen as editor

[whedon]

OK, the editor is @osorensen

[osorensen]

@AKUMAR0019, I'm now the editor for this submission. If you know of any potential reviewers, please mention their GitHub username in this thread (without the leading @).

[osorensen]

@whedon generate pdf

[whedon]

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

[osorensen]

@kasbohm, @devDonnn, @sealhuang, @snastase, @dr-xenia, would any of you be interested in reviewing this submission to the Journal of Open Source Software?

[AKUMAR0019]

@whedon list reviewers

[whedon]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[AKUMAR0019]

@AKUMAR0019, I'm now the editor for this submission. If you know of any potential reviewers, please mention their GitHub username in this thread (without the leading @).

Thank you @osorensen for agreeing to edit this paper!

A list of potential reviewers: robbisg htwangtw SRSteinkamp richford 62442katieb a3sha2 peerherholz Remi-Gau matteomancini dr-xenia mwegrzyn mih JonathanReardon sealhuang

[osorensen]

@robbisg @htwangtw @JonathanReardon would any of you be interested in reviewing this submission to the Journal of Open Source Software?

[htwangtw]

@osorensen I am interested but I am only available after the 17th of August. Is that okay?

[osorensen]

@htwangtw thanks, that's very ok!

[osorensen]

@whedon add @htwangtw as reviewer

[whedon]

OK, @htwangtw is now a reviewer

[robbisg]

I can review as well.