Joss-reviews: [PRE REVIEW]: emba: R package for analysis and visualization of biomarkers in boolean model ensembles

[whedon]

Submitting author: @bblodfon (John Zobolas)
Repository: https://github.com/bblodfon/emba
Version: v0.1.6
Editor: @mikldk
Reviewers: @sahilseth, @edifice1989
Managing EiC: Kristen Thyng

: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.

Author instructions

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

The author's suggestion for the handling editor is @csoneson.

@bblodfon 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.27 s (401.4 files/s, 84477.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            74           3562            951          11664
R                               16            443           2209           1799
TeX                              1             36              0            456
CSS                              3             99             48            428
JavaScript                       5             65             37            277
Markdown                         5             77              0            240
XML                              1              0              0            201
Rmd                              1            105            237            132
YAML                             3              6              1             64
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           110           4393           3484          15272
-------------------------------------------------------------------------------


Statistical information for the repository '2534' was gathered on 2020/07/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
john                             3           391              0          100.00

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
john                        391          100.0          0.0                9.97

[whedon]

Reference check summary:

OK DOIs

- 10.3389/fgene.2016.00094 is OK
- 10.1038/ncb1497 is OK
- 10.1038/nbt.2284 is OK
- 10.1186/s12859-016-1287-z is OK
- 10.1158/0008-5472.CAN-17-0078 is OK
- 10.1371/journal.pcbi.1004426 is OK
- 10.1016/J.CELS.2018.10.013 is OK
- 10.1186/1752-0509-6-96 is OK
- 10.1093/bioinformatics/btw682 is OK
- 10.1038/nmeth.2016 is OK
- 10.1021/bi902202q is OK
- 10.1093/bioinformatics/btq124 is OK
- 10.3389/fphys.2018.01605 is OK
- 10.3389/fphys.2018.00646 is OK
- 10.3389/fphys.2018.00680 is OK
- 10.1093/bioinformatics/btv013 is OK
- 10.1007/978-3-319-67471-1_20 is OK
- 10.1016/j.molmed.2017.08.003 is OK
- 10.1093/bioinformatics/btx123 is OK
- 10.1186/1752-0509-6-133 is OK
- 10.1002/psp4.12225 is OK
- 10.1088/1478-3975/9/5/055001 is OK
- 10.1186/s12864-019-6413-7 is OK
- 10.1093/bioinformatics/btaa561 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kthyng]

Hmm, all of our bioinformatics/genetics editors are pretty overloaded with submissions to handle. Do any of you feel able to take on this submission? @fboehm, @majensen, @will-rowe, @csoneson, @mikldk, @lpantano?

[mikldk]

@whedon assign me as editor

[whedon]

OK, the editor is @mikldk

[mikldk]

@tgerke, @jenzopr: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

[bblodfon]

Hi @mikldk,

Just a kindly remainder that there has been no response from the potential reviewers regarding this paper submission (maybe they are on vacations :)
Should we try to contact them again or try finding others?

[mikldk]

Indeed, @bblodfon - I was actually going to attend to this today.

[mikldk]

@mariacuellar, @sahilseth: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

[jenzopr]

Actually, I had left this unread, but then forgot to give feedback. Unfortunately, I'll not be able to conduct the review.

[mariacuellar]

I cannot at this time. Thank you for asking.

All the best,
Maria

On Thu, Aug 6, 2020 at 7:57 AM Jens Preußner [e-mail]
wrote:

Actually, I had left this unread, but then forgot to give feedback.
Unfortunately, I'll not be able to conduct the review.

—
You are receiving this because you were mentioned.
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>

Maria Cuellar, PhD
Assistant Professor
Criminology Department
University of Pennsylvania
http://web.sas.upenn.edu/mcuellar/

[mikldk]

@tgerke, @sahilseth, @JonathanReardon, @trinker: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

[bblodfon]

@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

[bblodfon]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[sahilseth]

Sure I can review, thanks

[mikldk]

@whedon assign @sahilseth as reviewer

[whedon]

OK, @sahilseth is now a reviewer

[mikldk]

We still need one reviewer. I have tried quite a few. @bblodfon, do you have any suggestions?

[bblodfon]

Hi @mikldk, I do not currently have any specific suggestions. Should we try more people from the volunteers list?

[mikldk]

@edifice1989, @jkanche: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

[edifice1989]

Sure! I am in!

Ming

On Wed, Aug 19, 2020 at 1:29 AM Mikkel Meyer Andersen <
[email protected]> wrote:

>
>

@edifice1989 https://github.com/edifice1989, @jkanche
https://github.com/jkanche: Would you be interested in reviewing this
submission to The Journal of Open Source Software
https://joss.theoj.org/? Reviews are open and based on a checklist. The
reviewer guidelines are available here:
https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you
have any questions or concerns please let me know.

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[mikldk]

@whedon add @edifice1989 as reviewer

[whedon]

OK, @edifice1989 is now a reviewer

[mikldk]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2583.

[edifice1989]

Hi Mikkel,

The invitation link has expired for me

https://github.com/openjournals/joss-reviews/invitations

Could you please resend it?

Thanks,
Ming

On Wed, Aug 19, 2020 at 5:24 AM Mikkel Meyer Andersen <
[email protected]> wrote:

@whedon https://github.com/whedon add @edifice1989
https://github.com/edifice1989 as reviewer

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[mikldk]

@edifice1989 Don't you have access over at the review in #2583?

[edifice1989]

Yes. I have. But I can't click the checklist for me.
When I click the invitation link, it says 'the link has expired'

On Thu, Aug 27, 2020 at 3:50 AM Mikkel Meyer Andersen <
[email protected]> wrote:

@edifice1989 https://github.com/edifice1989 Don't you have access over
at the review in #2583
https://github.com/openjournals/joss-reviews/issues/2583?

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