[PRE REVIEW]: Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral genomes with CpG dinucleotides

[editorialbot]

Submitting author: @oleksulkowski (Aleksander Sułkowski)
Repository: https://github.com/oleksulkowski/Syn-CpG-Spacer
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @fboehm
Reviewers: @babinyurii, @KatyBrown
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1edc7b46400b5b662030a231288cef97/status.svg)](https://joss.theoj.org/papers/1edc7b46400b5b662030a231288cef97)

Author instructions

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

@oleksulkowski 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 1.88  T=0.06 s (202.7 files/s, 182482.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1           1802              2           6393
Python                           2            175             77           1320
JavaScript                       2            175              0           1230
TeX                              1             10              0            162
SVG                              1              0              0            139
Markdown                         2             42              0             88
YAML                             3              8              4             46
JSON                             1              0              0             32
-------------------------------------------------------------------------------
SUM:                            13           2212             83           9410
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 697

[editorialbot]

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

OK DOIs

- 10.1146/annurev-virology-091919-104213 is OK
- 10.1186/1756-0500-5-50 is OK
- 10.18129/B9.bioc.SynMut is OK
- 10.1371/journal.ppat.1000079 is OK
- 10.1042/BST20200695 is OK
- 10.1128/spectrum.02529-23 is OK
- 10.1371/journal.ppat.1011357 is OK
- 10.7554/eLife.12735 is OK
- 10.1038/s41564-022-01223-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@oleksulkowski thanks for this submission. I am the AEiC for this track. Apologies for the initial delay encountered here.
I have just flagged this work with the query-scope label. This is because I need some help from the editorial board to determine if this work is in scope for JOSS. In particular we will review if this work conforms to our substantial scholarly effort criteria, and if it contains sufficient scientific research functionality to warrant a JOSS paper.

The scope review should take about 2 weeks to complete.

[oleksulkowski]

Thank you. The software has been developed since November 2022.

[Kevin-Mattheus-Moerman]

@oleksulkowski I have just removed the query-scope label as it was determined this work may be in scope for JOSS. I will now proceed to find a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @crsl4 as editor

[editorialbot]

Invitation to edit this submission sent!

[oleksulkowski]

Hi @crsl4!
Just wanted to send a friendly reminder after the holiday period. I appreciate your time and consideration.

[Kevin-Mattheus-Moerman]

@editorialbot invite @crsl4 as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@fboehm is this your cup of tea 🍵 ? Would you be able to help edit this one? Thanks!

[fboehm]

@Kevin-Mattheus-Moerman - thank you for hte invitation! Yes, I will edit this submission. Thank you again!

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[fboehm]

@warrenlr @babinyurii @nterhoeven @ramadatta @oschwengers - would you be willing to review this submission for JOSS? As you know, our reviews are checklist-driven, meaning that a reviewer will be given a checklist of items to assess for the software and accompanying short manuscript.

Please feel free to ask me any questions. Thank you for considering this invitation.

[babinyurii]

Hi, Frederick! Yes, I can review this submission. сб, 27 янв. 2024 г. в 18:58, Frederick Boehm ***@***.***>:

…

@warrenlr <https://github.com/warrenlr> @babinyurii <https://github.com/babinyurii> @nterhoeven <https://github.com/nterhoeven> @ramadatta <https://github.com/ramadatta> @oschwengers <https://github.com/oschwengers> - would you be willing to review this submission for JOSS? As you know, our reviews are checklist-driven, meaning that a reviewer will be given a checklist of items to assess for the software and accompanying short manuscript. Please feel free to ask me any questions. Thank you for considering this invitation. — Reply to this email directly, view it on GitHub <#6034 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AG3NDQJWLWBTOIJKWVF4TCLYQUPZPAVCNFSM6AAAAAA7CWCTHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTGIYDONBUGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[fboehm]

@editorialbot add @babinyurii as reviewer

[editorialbot]

@babinyurii added to the reviewers list!

[fboehm]

@babinyurii - thank you! I've now added you as a reviewer. Once we find a second reviewer, we'll officially start the review.

[fboehm]

@warrenlr @nterhoeven @ramadatta @oschwengers - would you be willing to review this submission for JOSS? As you know, our reviews are checklist-driven, meaning that a reviewer will be given a checklist of items to assess for the software and accompanying short manuscript.

Please feel free to ask me any questions. Thank you for considering this invitation.

[oleksulkowski]

Hi @fboehm, I've had a look at the JOSS reviewers list and I would like to suggest KatyBrown, ns-rse, ammaraziz, will-rowe and dsurujon (I removed the @ to avoid tagging them).

[fboehm]

@KatyBrown @ns-rse @ammaraziz @will-rowe @dsurujon - would you be willing to review this submission for JOSS? Our reviews are checklist-driven, meaning that a reviewer will be given a checklist of items to assess for the software and accompanying short manuscript. Please feel free to ask me questions :) Thank you for considering this invitation!

[fboehm]

@oleksulkowski - Thank you for the suggestions! I'm hopeful that we can find a reviewer in the next day or two. Once we do so, we can then officially start the "review". Thank you again!

[ns-rse]

I'm afraid I've got too much on at the moment to dedicate the necessary time I'm afraid, sorry.

[KatyBrown]

Hi @fboehm, I'm happy to review this.

[dsurujon]

@fboehm I'm also willing to review this submission

[fboehm]

Thank you, @ns-rse @KatyBrown @dsurujon for the helpful replies and offers to review. I'll assign @KatyBrown as the second reviewer for this submission. @ns-rse @dsurujon - I hope that we can work together on another review in the near future :)

[fboehm]

@editorialbot add @KatyBrown as reviewer

[editorialbot]

@KatyBrown added to the reviewers list!

[fboehm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6332.