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

[editorialbot]

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

Status

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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.

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[editorialbot]

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]

Paper file info:

📄 Wordcount for paper.md is 522

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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]

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

[birm]

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

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[birm]

@editorialbot check references

[editorialbot]

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]

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]

@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]

@birm 👋

[birm]

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]

@editorialbot invite @csoneson as editor

[editorialbot]

Invitation to edit this submission sent!

[csoneson]

@editorialbot assign @csoneson as editor

[editorialbot]

Assigned! @csoneson is now the editor

[csoneson]

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

[csoneson]

👋🏻 @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
#6700

Thanks in advance!

[allie-tatarian]

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]

@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]

@birm thanks - looks like it is working now!

[csoneson]

👋🏻 @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!

[csoneson]

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

[flekschas]

@csoneson Happy to review it!

[csoneson]

@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]

@editorialbot add @flekschas as reviewer

[editorialbot]

@flekschas added to the reviewers list!

[sebastian-raubach]

👋🏻 @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]

Awesome, thank you @sebastian-raubach!

[csoneson]

@editorialbot add @sebastian-raubach as reviewer

[editorialbot]

@sebastian-raubach added to the reviewers list!

[csoneson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6837.