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[PRE REVIEW]: Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration. #6700

Closed editorialbot closed 6 months ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@birm<!--end-author-handle-- (Ryan Birmingham) Repository: https://github.com/sharmalab/eaglescope Branch with paper.md (empty if default branch): Version: 1.0 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @flekschas, @sebastian-raubach Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/229f0d11e01fb7316ef9da35d9e466ae/status.svg)](https://joss.theoj.org/papers/229f0d11e01fb7316ef9da35d9e466ae)

Author instructions

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

@birm 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.

Editor instructions

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editorialbot commented 7 months ago

Hello human, 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:

@editorialbot generate pdf
editorialbot commented 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=1.06 s (1682.6 files/s, 234202.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                     101           6936          22483         133167
SVG                           1567              0             24          24921
JSON                            15              3              0          22546
CSS                             44           4888            551          21120
Sass                            19            519             34           4755
LESS                            18            504             55           4636
HTML                             8             69             53            673
CSV                              1              0              0            302
Markdown                         5             33              0            151
YAML                             5             15              4             79
TeX                              1              5              0             45
Dockerfile                       1              3              0             15
Bourne Shell                     1              0              0              3
-------------------------------------------------------------------------------
SUM:                          1786          12975          23204         212413
-------------------------------------------------------------------------------

Commit count by author:

   143  Ryan Birmingham
    32  Birm
    19  Yahia Zakaria
    17  Nan Li
     9  Jasox NaN
     7  Mohamed Nasser
     3  nanli-emory
     1  ArthurMor4is
     1  Pranav
     1  dependabot[bot]
editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 522

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 7 months ago

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

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Bokeh: an interactive visualization library for mo...
- 10.1126/scisignal.2004088 may be a valid DOI for title: Integrative analysis of complex cancer genomics an...
- 10.7287/peerj.preprints.26441v1 may be a valid DOI for title: DataScope: Interactive visual exploratory dashboar...
- 10.1038/s41598-020-60981-9 may be a valid DOI for title: NBIA: a network-based integrative analysis framewo...
- 10.1007/s10278-013-9622-7 may be a valid DOI for title: The Cancer Imaging Archive (TCIA): Maintaining and...
- 10.1200/cci.20.00001 may be a valid DOI for title: PRISM: A Platform for Imaging in Precision Medicin...

INVALID DOIs

- None
birm commented 7 months ago

I think we've fixed the dois! Not sure if Bokeh has a preferred citation though.

birm commented 7 months ago

@editorialbot commands

editorialbot commented 7 months ago

Hello @birm, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
birm commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1126/scisignal.2004088 is OK
- 10.1109/VAHC.2017.8387496 is OK
- 10.1038/s41598-020-60981-9 is OK
- 10.1007/s10278-013-9622-7 is OK
- 10.1200/cci.20.00001 is OK

MISSING DOIs

- No DOI given, and none found for title: Bokeh: an interactive visualization library for mo...

INVALID DOIs

- None
birm commented 6 months ago

Based on the interests on the reviewer form, I think Ian Hunt-Isaak and Allie Tatarian would be good reviewers for this paper.

Kevin-Mattheus-Moerman commented 6 months ago

@birm thanks for those suggestions. I am currently checking if this work is in scope for JOSS, and if so, will be looking for a handling editor shortly.

In the mean time, can you help clarify if it would be correct to say that the JavaScript for this submission forms the main code achievement here? Secondly, could you clarify if the JavaScript is fully your original work, or if some default (e.g. GUI related) codes were imported or if code was autogenerated. Thanks.

Kevin-Mattheus-Moerman commented 6 months ago

@birm :wave:

birm commented 6 months ago

Sorry for the delay. The code is the accomplishment. It uses react, but it's otherwise the contrubutors' work. The only part which is autogenerated is in ./dist/, which we prebuild for the demo site (https://sharmalab.github.io/eaglescope/) and other deployments where we don't have something to bundle the code.

Kevin-Mattheus-Moerman commented 6 months ago

@editorialbot invite @csoneson as editor

editorialbot commented 6 months ago

Invitation to edit this submission sent!

csoneson commented 6 months ago

@editorialbot assign @csoneson as editor

editorialbot commented 6 months ago

Assigned! @csoneson is now the editor

csoneson commented 6 months ago

👋🏻 @birm I will handle your submission and will start by finding two suitable reviewers. Thank you for the suggestions above.

csoneson commented 6 months ago

👋🏻 @ianhi, @allie-tatarian - would you be interested in reviewing this submission for JOSS?

Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration https://github.com/openjournals/joss-reviews/issues/6700

Thanks in advance!

allie-tatarian commented 6 months ago

Hi @csoneson, thanks for reaching out! I actually can't get this software to run on my machine at all - I think it might be a security issue (this has happened to me before). I've attached the error log in case it's useful to the developers (@birm), but I'm going to let someone else review this one. 2024-05-31T16_28_22_532Z-debug-0.log

birm commented 6 months ago

@allie-tatarian Thank you for the log! I think we fixed that dependency just now. Even if you can't review, would you be able to try running it again to see if this has resolved your issue. Your help is appreciated either way!

allie-tatarian commented 6 months ago

@birm thanks - looks like it is working now!

csoneson commented 6 months ago

👋🏻 @flekschas, @sebastian-raubach - would you be interested in reviewing this submission for JOSS?

Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration https://github.com/openjournals/joss-reviews/issues/6700

Thanks in advance!

csoneson commented 6 months ago

Hi @allie-tatarian - thanks for your quick response (and the error log 🙂).

flekschas commented 6 months ago

@csoneson Happy to review it!

csoneson commented 6 months ago

@flekschas Thank you! I will assign you, and as soon as we have secured one more reviewer I will open the actual review issue where you will be able to generate your review checklist.

csoneson commented 6 months ago

@editorialbot add @flekschas as reviewer

editorialbot commented 6 months ago

@flekschas added to the reviewers list!

sebastian-raubach commented 6 months ago

👋🏻 @flekschas, @sebastian-raubach - would you be interested in reviewing this submission for JOSS?

Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration

6700

Thanks in advance!

Yeah, I can give it a go.

csoneson commented 6 months ago

Awesome, thank you @sebastian-raubach!

csoneson commented 6 months ago

@editorialbot add @sebastian-raubach as reviewer

editorialbot commented 6 months ago

@sebastian-raubach added to the reviewers list!

csoneson commented 6 months ago

@editorialbot start review

editorialbot commented 6 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6837.