[REVIEW]: RNMC: kinetic Monte Carlo implementations for complex reaction networks #7244

editorialbot · 2024-09-18T10:57:48Z

Submitting author: @espottesmith (Evan Spotte-Smith)
Repository: https://github.com/BlauGroup/RNMC
Branch with paper.md (empty if default branch):
Version: v1.1.1
Editor: @mbarzegary
Reviewers: @Anshuman5, @ptmerz, @lorenzo-rovigatti
Archive: 10.5281/zenodo.14360064

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7d071341934be452863d5523edb17413"><img src="https://joss.theoj.org/papers/7d071341934be452863d5523edb17413/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7d071341934be452863d5523edb17413/status.svg)](https://joss.theoj.org/papers/7d071341934be452863d5523edb17413)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@Anshuman5 & @ptmerz & @lorenzo-rovigatti, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mbarzegary know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @Anshuman5

📝 Checklist for @lorenzo-rovigatti

📝 Checklist for @ptmerz

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-09-18T10:57:53Z

Hello humans, 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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2024-09-18T10:58:20Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.34 s (246.9 files/s, 39609.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             26           1091            558           4470
C/C++ Header                    27            618            354           2236
Jupyter Notebook                 5              0           1178           1479
SVG                              1              0              0            308
make                             4             86             85            162
Markdown                         3             31              0            147
TeX                              1             11              0            114
Ruby                             1             28             12            106
Bourne Shell                     2             23              2             71
Nix                              2              8              4             63
YAML                             2              1              4             34
JSON                             9              0              0             32
-------------------------------------------------------------------------------
SUM:                            83           1897           2197           9222
-------------------------------------------------------------------------------

Commit count by author:

   229	Laura Zichi
   174	Daniel Barter
    28	Evan Walter Clark Spotte-Smith
    28	lzichi
    16	Evan Walter Clark Spotte-Smith, PhD

editorialbot · 2024-09-18T10:58:24Z

Paper file info:

📄 Wordcount for paper.md is 964

✅ The paper includes a Statement of need section

editorialbot · 2024-09-18T10:58:26Z

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot · 2024-09-18T10:58:29Z

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

✅ OK DOIs

- 10.1021/acs.nanolett.3c01955 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Exact stochastic simulation of coupled chemical re...
- No DOI given, and none found for title: Crossing the mesoscale no-mans land via parallel k...
- No DOI given, and none found for title: Electrochemical Systems

❌ MISSING DOIs

- 10.1063/1.1696792 may be a valid DOI for title: On the theory of electron-transfer reactions. VI. ...
- 10.1016/j.cpc.2014.04.003 may be a valid DOI for title: kmos: A lattice kinetic Monte Carlo framework
- 10.1021/acsenergylett.2c00517.s001 may be a valid DOI for title: Toward a Mechanistic Model of Solid–Electrolyte In...
- 10.26434/chemrxiv-2021-c2gp3-v2 may be a valid DOI for title: Predictive stochastic analysis of massive filter-b...
- 10.1021/jacs.3c02222.s001 may be a valid DOI for title: Chemical reaction networks explain gas evolution m...
- 10.1021/acs.nanolett.3c03568.s001 may be a valid DOI for title: Accelerating the Design of Multishell Upconverting...
- 10.1039/c4cs00205a may be a valid DOI for title: Combinatorial approaches for developing upconverti...
- 10.1021/acs.jpcc.9b00161.s001 may be a valid DOI for title: Energy transfer networks within upconverting nanop...

❌ INVALID DOIs

- None

mbarzegary · 2024-09-18T10:59:45Z

👋🏼 @Anshuman5, @lorenzo-rovigatti, @ptmerz this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews/issues/7244 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread.

We aim for reviews to be completed within about 4-6 weeks. Please feel free to ping me (@mbarzegary) if you have any questions/concerns.

editorialbot · 2024-09-18T10:59:51Z

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

mbarzegary · 2024-09-18T11:01:53Z

@espottesmith this is where the review takes place. Please keep an eye out for comments here from the reviewers, as well as any issues opened by them on your software repository. I recommend you aim to respond to these as soon as possible, and you can address them straight away as they come in if you like, to ensure we do not loose track of the reviewers.

To start, can you please fix the DOIs issue raised by the editorial bot above?

Anshuman5 · 2024-09-19T15:36:14Z

Review checklist for @Anshuman5

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/BlauGroup/RNMC?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@espottesmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

espottesmith · 2024-09-19T18:28:17Z

All available DOIs should be present now.

lorenzo-rovigatti · 2024-09-21T06:02:33Z

Review checklist for @lorenzo-rovigatti

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/BlauGroup/RNMC?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@espottesmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

lorenzo-rovigatti · 2024-09-22T11:47:27Z

I have added a couple of issues to the repo. For now I can't install the software and therefore I can't test it, but I have read the paper and I found it good, apart from the following two issues:

Authorship: the list of authors is rather long compared to the people who are listed as contributors. Do all authors comply with the JOSS policies on authorship?
Software extensibility: the paper states that RNMC has been designed "to be easily extensible". Can you clarify this statement in the paper and perhaps in the documentation, which lacks a section on this matter?

ptmerz · 2024-09-30T02:16:08Z

Review checklist for @ptmerz

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/BlauGroup/RNMC?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@espottesmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

ptmerz · 2024-09-30T03:14:46Z

First part of my review, unfortunately I ran out of time today and will continue in the next days.

License: While the license looks like an appropriate open source license, I didn't succeed on finding it on https://opensource.org/licenses/alphabetical as requested by the checklist. If it is on the list, can you point me to it?
Contributors: As @lorenzo-rovigatti mentioned, we can only verify three of the authors (Laura Zichi, Daniel Barter, and @espottesmith) from the repo. Can you please comment on your choices for the author list?
Installation: While I could install the software without issues in one of the described ways, the other described way failed with a non-descriptive error. The underlying problem is very minor, but the resulting error can be confusing and time consuming. I opened an issue at [JOSS review] Installation of single module requires previous folder creation BlauGroup/RNMC#15.

ptmerz · 2024-09-30T03:22:49Z

And a quick note on the references in the paper: Some of the references in the text are rendered a bit weirdly. Several references either lack a space between the previous word and the parenthesis like this

Marcus theory(Marcus, 1965)

or they are rendered after the period or comma rather than before:

Butler-Volmer kinetics.(Newman & Balsara, 2021)

A quick look at recent publications (https://joss.theoj.org) confirm that they should be rendered with a space and before any period or comma.

espottesmith · 2024-10-04T20:35:12Z

Hey, I'll be addressing these questions/comments piecemeal.

First, references should be fixed.

Regarding the license, we're using the BSD-3-Clause-LBNL license. From https://spdx.org/licenses/BSD-3-Clause-LBNL.html:

This license is the same as BSD-3-Clause, but with an additional default contribution licensing clause

espottesmith · 2024-10-07T16:42:43Z

Regarding authorship:

Eric Sivonxay (@sivonxay) wrote most of the NPMC simulator for nanoparticle photophysics. He opened a PR ([WIP] Merge NPMC changes back into main branch BlauGroup/RNMC#3), but we ultimately decided that it'd be easier if @lzichi just took his code and did the work of unifying the various simulators.
Rohith Srinivaas Mohanakrishnan (@rohithsrinivaas) did a lot of testing and contributed to bugfixes. He was particularly helpful for testing and developing LGMC. He also worked on some code for visualization and analysis, but this code hasn't been integrated into RNMC yet.
Emory M. Chan (not sure he's on GitHub?) provided code for nanoparticle simulations to Eric, which eventually became NPMC. He also provided direct technical guidance for the development of NPMC.
Kristin A. Persson (also not on GitHub?) provided technical mentorship to several members of this team, including myself, Laura Zichi, and Rohith Srinivaas
Samuel M. Blau (@samblau) conceived of the idea of RNMC, directed its development from inception, and provided technical guidance to most of the developers. I'm sure he also did some amount of testing, code review, etc., though @danielbarter might be able to speak to that with more detail.

espottesmith · 2024-10-09T14:58:41Z

Installation issues should now be fixed, thanks to @lzichi.

To @lorenzo-rovigatti's point about extending RNMC, there's also now a page in the documentation on expanding RNMC, which is linked in the page for contributors. I can add a brief section in the manuscript as well.

espottesmith · 2024-10-17T12:37:06Z

Hey, just wanted to bump this. @ptmerz @lorenzo-rovigatti have your comments/issues been addressed? @Anshuman5 have you had a chance to read and evaluate the code/paper?

Anshuman5 · 2024-10-18T02:03:36Z

@espottesmith thanks for checking. I would be able to review this by early next week.

Anshuman5 · 2024-10-24T20:10:36Z

This work presents a highly valuable tool for the scientific community by providing a program for kMC simulation for modeling complex systems. I strongly recommend publication after addressing the following:

include current limitation of RNMC - for example, limited to simulating reactions upto two reactants and two products, in the draft or readme.md file.
in the documentation under GMC - Running GMC, include the sample output file names, logs, and directories that will be generated after running the command build/GMC --reaction_database=examples/GMC/end-to-end-test/.... Do the same for other sections - NPMC and LGMC.
RNMC is not expanded in the Summary section of the draft (line no.21).
Change the color of text 'RNMC' in logo.png. It is not clearly visible when opening github in dark mode. See
image.

mbarzegary · 2024-11-25T10:35:09Z

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

Read the text of the paper and offer comments/corrections (as either a list or a pull request)
Check that the archive title, author list, version tag, and the license are correct
Set archive DOI with @editorialbot set <DOI here> as archive
Set version with @editorialbot set <version here> as version
Double check rendering of paper with @editorialbot generate pdf
Specifically check the references with @editorialbot check references and ask author(s) to update as needed
Recommend acceptance with @editorialbot recommend-accept

mbarzegary · 2024-11-25T10:36:13Z

@espottesmith given the green light of the reviewers, we will now work towards processing this for acceptance in JOSS. So please

Merge my PR with some minor edits
Work on the author's points of the final checklist I created ☝️

I can then move forward with recommending acceptance of the submission.

espottesmith · 2024-11-25T13:36:06Z

Thank you @mbarzegary!

I've merged in your PR, and in response to your checklist above:

Authors and affiliations are correct
The most recent release, which includes all changes related to this review, is https://github.com/BlauGroup/RNMC/releases/tag/v1.1.0
There's currently an issue with the RNMC Zenodo (https://zenodo.org/records/7277767), and recent releases haven't been posted and archived there. I'll work to get that sorted as soon as possible. Once I am able to post releases there, I'll also update the author list and license. The DOI is and will be https://doi.org/10.5281/zenodo.7277766

espottesmith · 2024-11-25T13:37:30Z

@editorialbot generate pdf

editorialbot · 2024-11-25T13:39:29Z

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

mbarzegary · 2024-12-01T18:02:56Z

@espottesmith okay, no problem. We will proceed with the acceptance when the archive issue is resolved. We need the DOI for the mentioned version.

mbarzegary · 2024-12-01T18:03:26Z

@editorialbot set v1.1.0 as version

editorialbot · 2024-12-01T18:03:29Z

Done! version is now v1.1.0

espottesmith · 2024-12-10T13:56:26Z

Hey @mbarzegary, sorry for the delay.

I wasn't able to get v1.1.0 onto Zenodo because of some permission issues, but I was able to release a new version and get v1.1.1 archived. The DOI is 10.5281/zenodo.14360064.

I've updated the title and author list to match the paper, and the licenses match.

Please let me know if there's anything else you need to move this process forward!

mbarzegary · 2024-12-13T13:15:02Z

@editorialbot set v1.1.1 as version

editorialbot · 2024-12-13T13:15:06Z

Done! version is now v1.1.1

mbarzegary · 2024-12-13T13:15:34Z

@editorialbot set 10.5281/zenodo.14360064 as archive

editorialbot · 2024-12-13T13:15:37Z

Done! archive is now 10.5281/zenodo.14360064

mbarzegary · 2024-12-13T13:16:16Z

@editorialbot recommend-accept

editorialbot · 2024-12-13T13:16:18Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-12-13T13:16:42Z

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

✅ OK DOIs

- 10.1063/1.1696792 is OK
- 10.1016/j.cpc.2014.04.003 is OK
- 10.1021/acsenergylett.2c00517 is OK
- 10.1039/D2DD00117A is OK
- 10.1021/jacs.3c02222 is OK
- 10.1021/acs.nanolett.3c03568 is OK
- 10.1039/C4CS00205A is OK
- 10.1021/acs.nanolett.3c01955 is OK
- 10.1021/acs.jpcc.9b00161 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Exact stochastic simulation of coupled chemical re...
- No DOI given, and none found for title: Crossing the mesoscale no-mans land via parallel k...
- No DOI given, and none found for title: Electrochemical Systems

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-12-13T13:18:40Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6252, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-12-17T08:31:26Z

Kevin-Mattheus-Moerman · 2024-12-17T08:31:35Z

@editorialbot accept

editorialbot · 2024-12-17T08:31:37Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-12-17T08:38:45Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Zichi
  given-names: Laura
  orcid: "https://orcid.org/0000-0003-3897-3097"
- family-names: Barter
  given-names: Daniel
  orcid: "https://orcid.org/0000-0002-6408-1255"
- family-names: Sivonxay
  given-names: Eric
  orcid: "https://orcid.org/0000-0002-6408-1255"
- family-names: Spotte-Smith
  given-names: Evan Walter Clark
  orcid: "https://orcid.org/0000-0003-1554-197X"
- family-names: Mohanakrishnan
  given-names: Rohith Srinivaas
- family-names: Chan
  given-names: Emory M.
- family-names: Persson
  given-names: Kristin Aslaug
- family-names: Blau
  given-names: Samuel M.
contact:
- family-names: Persson
  given-names: Kristin Aslaug
- family-names: Blau
  given-names: Samuel M.
doi: 10.5281/zenodo.14360064
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zichi
    given-names: Laura
    orcid: "https://orcid.org/0000-0003-3897-3097"
  - family-names: Barter
    given-names: Daniel
    orcid: "https://orcid.org/0000-0002-6408-1255"
  - family-names: Sivonxay
    given-names: Eric
    orcid: "https://orcid.org/0000-0002-6408-1255"
  - family-names: Spotte-Smith
    given-names: Evan Walter Clark
    orcid: "https://orcid.org/0000-0003-1554-197X"
  - family-names: Mohanakrishnan
    given-names: Rohith Srinivaas
  - family-names: Chan
    given-names: Emory M.
  - family-names: Persson
    given-names: Kristin Aslaug
  - family-names: Blau
    given-names: Samuel M.
  date-published: 2024-12-17
  doi: 10.21105/joss.07244
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7244
  title: "RNMC: kinetic Monte Carlo implementations for complex reaction
    networks"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07244"
  volume: 9
title: "RNMC: kinetic Monte Carlo implementations for complex reaction
  networks"

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editorialbot · 2024-12-17T08:38:50Z

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

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Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07244 joss-papers#6258
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Kevin-Mattheus-Moerman · 2024-12-17T08:52:23Z

@espottesmith congratulations on this JOSS publication!

@mbarzegary thanks for editing!

And a special thank you to the reviewers: @Anshuman5, @ptmerz, @lorenzo-rovigatti !!

editorialbot · 2024-12-17T08:52:25Z

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editorialbot added C++ Makefile review Ruby Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 18, 2024

editorialbot assigned mbarzegary Sep 18, 2024

editorialbot mentioned this issue Sep 18, 2024

[PRE REVIEW]: RNMC: kinetic Monte Carlo implementations for complex reaction networks #7159

Closed

This was referenced Sep 22, 2024

[JOSS review] Installation issues BlauGroup/RNMC#12

Closed

[JOSS review] Some information missing BlauGroup/RNMC#13

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 13, 2024

editorialbot added accepted published Papers published in JOSS labels Dec 17, 2024

Kevin-Mattheus-Moerman closed this as completed Dec 17, 2024

[REVIEW]: RNMC: kinetic Monte Carlo implementations for complex reaction networks #7244

[REVIEW]: RNMC: kinetic Monte Carlo implementations for complex reaction networks #7244

Comments

editorialbot commented Sep 18, 2024 • edited Loading

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Reviewer instructions & questions

Checklists

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mbarzegary commented Sep 18, 2024

Anshuman5 commented Sep 19, 2024 • edited Loading

Review checklist for @Anshuman5

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

espottesmith commented Sep 19, 2024

lorenzo-rovigatti commented Sep 21, 2024 • edited Loading

Review checklist for @lorenzo-rovigatti

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lorenzo-rovigatti commented Sep 22, 2024 • edited Loading

ptmerz commented Sep 30, 2024 • edited Loading

Review checklist for @ptmerz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ptmerz commented Sep 30, 2024

ptmerz commented Sep 30, 2024 • edited Loading

espottesmith commented Oct 4, 2024

espottesmith commented Oct 7, 2024

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Anshuman5 commented Oct 18, 2024

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Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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espottesmith commented Dec 10, 2024

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Kevin-Mattheus-Moerman commented Dec 17, 2024

Checks on repository

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editorialbot commented Sep 18, 2024 •

edited

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Anshuman5 commented Sep 19, 2024 •

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lorenzo-rovigatti commented Sep 21, 2024 •

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lorenzo-rovigatti commented Sep 22, 2024 •

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ptmerz commented Sep 30, 2024 •

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Anshuman5 commented Oct 24, 2024 •

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