[PRE REVIEW]: ProtoSyn.jl: a novel platform for computational molecular manipulation and simulation with a focus on protein design

[whedon]

Submitting author: @JosePereiraUA Repository: https://github.com/sergio-santos-group/ProtoSyn.jl Version: Editor: @odow Reviewers: @jgreener64, @mfherbst Managing EiC: Valentin Churavy

Author instructions

Thanks for submitting your paper to JCON @https://github.com/JosePereiraUA. Currently, there isn't an JCON editor assigned to your paper.

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

@https://github.com/JosePereiraUA 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 JCON and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JCON 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.

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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]

Failed to discover a Statement of need section in paper

[whedon]

Wordcount for paper.tex is 3356

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.36 s (892.3 files/s, 197451.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          162           4905           2050          21193
YAML                            54             16             28           2757
TeX                              8            263            177           2558
Markdown                        74            857              0           2015
TOML                             2            227              1           1039
Jupyter Notebook                17              0          32062            712
Lisp                             2             74              0            326
Python                           2             36             13            105
Ruby                             1              8              4             45
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           323           6386          34335          30751
-------------------------------------------------------------------------------

Statistical information for the repository '458f2ec4420f5141cff0e631' was
gathered on 2022/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
JosePereiraUA                    8           954           3262           34.81
José Pereira                     1            57              0            0.47
Sergio M. Santos                 6          3973           3864           64.72

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
José Pereira                102          178.9          7.9                6.86
Sergio M. Santos            109            2.7          0.0               10.09

[whedon]

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

OK DOIs

- 10.1038/nbt0798-617 is OK
- 10.1146/annurev.biophys.37.032807.125832 is OK
- 10.1038/nature19946 is OK
- 10.1002/pro.4098 is OK
- 10.1126/science.1089427 is OK
- 10.1093/bioinformatics/btq007 is OK
- 10.1038/s41592-020-0848-2 is OK
- 10.1038/s41586-019-1923-7 is OK
- 10.1038/s41586-021-03828-1 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1073/pnas.1914677117 is OK
- 10.1002/pro.3235 is OK
- 10.1007/978-1-4939-6637-0_2 is OK
- 10.26682/sjuod.2019.22.1.11 is OK
- 10.1371/journal.pone.0020161 is OK
- 10.1002/jcc.20727 is OK
- 10.1137/141000671 is OK
- 10.1145/3276490 is OK
- 10.1007/978-1-4613-8476-2_1 is OK
- 10.1002/CBIC.202000437 is OK
- 10.1093/BIOINFORMATICS/BTU106 is OK
- 10.1145/3276483 is OK
- 10.1073/pnas.96.10.5486 is OK

MISSING DOIs

- 10.1002/(sici)1097-0134(1999)37:3+<171::aid-prot21>3.0.co;2-z may be a valid DOI for title: Ab initio protein structure prediction of CASP III targets using ROSETTA

INVALID DOIs

- None

[whedon]

PDF failed to compile for issue #106 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

[carstenbauer]

@whedon assign @odow as editor

[odow]

@JosePereiraUA you're missing the https://github.com/JuliaCon/JuliaConSubmission.jl/blob/master/paper/.latexmkrc file from the template repository.

Do you have any suggestions for reviewers?

[JosePereiraUA]

I've added the .latexmkrc file in this commit.

From the above-mentioned list, and based on the descriptions provided, sloede seems to have some experience with numerical simulations. Besides that, I'd suggest anyone from the MolSim community.

A question: it seems the bot failed to find one of the DOI in my literature references, is there any action I have to take?

Thank you for your time! Cheers

[odow]

@whedon generate pdf

[whedon]

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

[odow]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/nbt0798-617 is OK
- 10.1146/annurev.biophys.37.032807.125832 is OK
- 10.1038/nature19946 is OK
- 10.1002/pro.4098 is OK
- 10.1126/science.1089427 is OK
- 10.1093/bioinformatics/btq007 is OK
- 10.1038/s41592-020-0848-2 is OK
- 10.1038/s41586-019-1923-7 is OK
- 10.1038/s41586-021-03828-1 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1073/pnas.1914677117 is OK
- 10.1002/pro.3235 is OK
- 10.1007/978-1-4939-6637-0_2 is OK
- 10.26682/sjuod.2019.22.1.11 is OK
- 10.1371/journal.pone.0020161 is OK
- 10.1002/jcc.20727 is OK
- 10.1137/141000671 is OK
- 10.1145/3276490 is OK
- 10.1007/978-1-4613-8476-2_1 is OK
- 10.1002/CBIC.202000437 is OK
- 10.1093/BIOINFORMATICS/BTU106 is OK
- 10.1145/3276483 is OK
- 10.1073/pnas.96.10.5486 is OK

MISSING DOIs

- 10.1002/(sici)1097-0134(1999)37:3+<171::aid-prot21>3.0.co;2-z may be a valid DOI for title: Ab initio protein structure prediction of CASP III targets using ROSETTA

INVALID DOIs

- None

[odow]

@sloede and @jgreener64 are you interested in reviewing this paper for the JuliaCon proceedings?

The submission I'd like you to review is titled: "ProtoSyn.jl: a novel platform for computational molecular manipulation and simulation with a focus on protein design". You can find more information at the top of this Github issue (https://github.com/JuliaCon/proceedings-review/issues/106).

The review process at JuliaCon is based on JOSS: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a seperate thread. In that thread, there will be a check list for each reviewer.

Given the lead-up to Christmas, our deadline for the first round isn't until the end of January, so there's no expectation that you'll start the review now if you are busy. I just need an indication that you're willing, otherwise I will need to find other reviewers. If you're willing, I'll ping you again in early January with a reminder.

[sloede]

I already agreed to reviewing two JC proceedings papers, thus I would prefer if someone else could do this one.

[odow]

No problem

[jgreener64]

Yes I am happy to do it.

[odow]

@whedon add @jgreener64 as reviewer

[whedon]

OK, @jgreener64 is now a reviewer

[odow]

@mfherbst are you interested in reviewing this paper for JuliaCon? Or alternatively, do you have suggestions for other reviewers?

[mfherbst]

Sure, why not. I should add though that my next few weeks are super tight, so I don't think I'll manage this before mid March.

[odow]

@whedon add @mfherbst as reviewer

[whedon]

OK, @mfherbst is now a reviewer

[odow]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/JuliaCon/proceedings-review/issues/124.