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[PRE REVIEW]: oxDNA: coarse-grained simulations of nucleic acids made simple
Submitting author: @lorenzo-rovigatti (Lorenzo Rovigatti) Repository: https://github.com/lorenzo-rovigatti/oxDNA Branch with paper.md (empty if default branch): joss_submission Version: v3.2.2 Editor: @ppxasjsm Reviewers: Pending Managing EiC: Daniel S. Katz
Status
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HTML: <a href="https://joss.theoj.org/papers/8d6e993a2bb0efa6fc9f9c76f48caf58"><img src="https://joss.theoj.org/papers/8d6e993a2bb0efa6fc9f9c76f48caf58/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/8d6e993a2bb0efa6fc9f9c76f48caf58)
Author instructions
Thanks for submitting your paper to JOSS @lorenzo-rovigatti. Currently, there isn't a JOSS editor assigned to your paper.
@lorenzo-rovigatti 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 @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:
@editorialbot commands
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:
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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
github.com/AlDanial/cloc v 1.88 T=1.12 s (959.2 files/s, 216520.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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C/C++ Header 395 16994 13215 74871
C++ 293 10277 7176 40624
Python 186 6337 4629 25795
CUDA 53 2841 1345 11860
C 2 378 1463 5747
Markdown 46 1005 0 3383
reStructuredText 30 1956 2331 3296
CMake 23 317 368 1609
XML 3 0 0 1187
SVG 2 0 0 854
CSS 2 182 49 775
TeX 4 56 2 400
YAML 8 35 27 388
Bourne Shell 14 68 44 283
INI 4 0 0 98
Cython 1 18 14 87
Jupyter Notebook 1 0 155 38
DOS Batch 1 8 1 26
make 2 5 9 24
TOML 1 0 0 8
JSON 4 0 0 4
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SUM: 1075 40477 30828 171357
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gitinspector failed to run statistical information for the repository
👋 @lorenzo-rovigatti - note that your paper does not compile.
The error includes "found a tab character that violate indentation while scanning a plain scalar at line 10 column 11"
Please follow the example paper. Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.
Hi! Thanks for considering oxDNA for publication. I hope I fixed the issues with the paper (which, strangely enough, does get compiled without any issues by the CI action). Possible referees (taken from the list): ptmerz, govarguz, marshallmcdonnell, RainierBarrett
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1039/B719370J is OK
- 10.1103/PhysRevE.99.032414 is OK
- 10.3389/fmolb.2021.693710 is OK
- 10.1039/C3CP53545B is OK
- 10.1063/1.4881424 is OK
- 10.1063/1.2790421 is OK
- 10.1140/epje/i2018-11669-8 is OK
- 10.1103/PhysRevLett.100.020603 is OK
- 10.1093/nar/gkaa200 is OK
- 10.1093/nar/gkaa593 is OK
- 10.1093/nar/gkab324 is OK
- 10.4230/LIPIcs.DNA.2020.9 is OK
- 10.4230/LIPIcs.DNA.27.5 is OK
- 10.1088/0953-8984/21/46/463102 is OK
MISSING DOIs
- 10.1093/nar/gkaa417 may be a valid DOI for title: Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
INVALID DOIs
- https://doi.org/10.1016/j.sbi.2015.11.011 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0009-2614(99)01123-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jcc.26029 is INVALID because of 'https://doi.org/' prefix
@lorenzo-rovigatti - I see a bunch of references (most of them) that are missing a space before them.
In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.
Also, in some areas (including this one), we have a small backlog of submissions and the most appropriate editor is already rather busy.
For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1039/B719370J is OK
- 10.1103/PhysRevE.99.032414 is OK
- 10.1016/j.sbi.2015.11.011 is OK
- 10.3389/fmolb.2021.693710 is OK
- 10.1039/C3CP53545B is OK
- 10.1063/1.4881424 is OK
- 10.1063/1.2790421 is OK
- 10.1140/epje/i2018-11669-8 is OK
- 10.1016/S0009-2614(99)01123-9 is OK
- 10.1103/PhysRevLett.100.020603 is OK
- 10.1093/nar/gkaa200 is OK
- 10.1093/nar/gkaa593 is OK
- 10.1002/jcc.26029 is OK
- 10.1093/nar/gkab324 is OK
- 10.4230/LIPIcs.DNA.2020.9 is OK
- 10.4230/LIPIcs.DNA.27.5 is OK
- 10.1093/nar/gkaa417 is OK
- 10.1088/0953-8984/21/46/463102 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi! I understand it's holiday time, but I was wondering if there was any update on a possible editor for this submission. Thank you!
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
