[PRE REVIEW]: cellular_raza: Cellular Agent-based Modeling from a Clean Slate #7520

editorialbot · 2024-11-23T20:49:21Z

Submitting author: @jonaspleyer (Jonas Pleyer)
Repository: https://github.com/jonaspleyer/cellular_raza
Branch with paper.md (empty if default branch): paper
Version: 0.1.6
Editor: @mahfuz05062
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7a0a13c37e57776edc21132f518ef36a"><img src="https://joss.theoj.org/papers/7a0a13c37e57776edc21132f518ef36a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7a0a13c37e57776edc21132f518ef36a/status.svg)](https://joss.theoj.org/papers/7a0a13c37e57776edc21132f518ef36a)

Author instructions

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

editorialbot · 2024-11-23T20:49:23Z

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:

@editorialbot generate pdf

editorialbot · 2024-11-23T20:49:37Z

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

✅ OK DOIs

- 10.3389/fphy.2022.968409 is OK
- 10.1016/j.cosrev.2017.03.001 is OK
- 10.1145/327070.327215 is OK
- 10.1006/jtbi.1997.0462 is OK
- 10.1016/S0378-4371(97)00511-6 is OK
- 10.1371/journal.pbio.0060141 is OK
- 10.1038/s41467-017-02285-7 is OK
- 10.1098/rstb.1952.0012 is OK
- 10.1177/00375497211068820 is OK
- 10.1104/pp.110.167619 is OK
- 10.1016/j.bpj.2013.11.4498 is OK
- 10.1371/journal.pcbi.1005569 is OK
- 10.1126/science.141.3579.401 is OK
- 10.1103/physrevlett.69.2013 is OK
- 10.1128/mmbr.00001-06 is OK
- 10.1111/j.1574-6976.2007.00098.x is OK
- 10.1038/ncomms15370 is OK
- 10.21105/joss.01848 is OK
- 10.1093/bioinformatics/btu498 is OK
- 10.1093/bioinformatics/btab649 is OK
- 10.1091/mbc.e16-01-0013 is OK
- 10.1002/cso2.1032 is OK
- 10.1038/ncomms13929 is OK
- 10.1038/ncomms13929 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: jonaspleyer/cr_trichome
- No DOI given, and none found for title: NetLogo

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-11-23T20:49:38Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (500.2 files/s, 98548.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             72              0            352
TeX                              1             25              0            333
Bourne Shell                     1              0              0              6
-------------------------------------------------------------------------------
SUM:                             4             97              0            691
-------------------------------------------------------------------------------

Commit count by author:

     2	Jonas Pleyer

editorialbot · 2024-11-23T20:49:42Z

Paper file info:

📄 Wordcount for paper.md is 2826

✅ The paper includes a Statement of need section

editorialbot · 2024-11-23T20:49:43Z

License info:

🔴 Failed to discover a valid open source license

editorialbot · 2024-11-23T20:50:54Z

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

editorialbot · 2024-11-23T20:51:38Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

danielskatz · 2024-11-23T21:19:38Z

👋 @jonaspleyer - Thanks for your submission.

However, note that your paper is about 3 times longer than the maximum recommended JOSS paper length. Please take a at the example paper. Please use the command @editorialbot generate pdf after making changes to the .md file to make a new PDF. You can also use the command @editorialbot check references to check a number of things, including the paper length. editorialbot commands need to be the first entry in a new comment.

In addition, the branch with your paper does not seem to include the software as well, but only has the paper. Typically, the paper branch is the same as the main branch, with the addition of the paper. Can you fix this?

jonaspleyer · 2024-11-23T23:38:18Z

@danielskatz Thanks for initiating the pre-review process. I was aware that my paper is longer than the expected maximum size. I am very happy to trim it down. Is it reasonable to make this decision via the review process or would you like me to make these changes before advancing?

jonaspleyer · 2024-11-23T23:38:20Z

@editorialbot commands

editorialbot · 2024-11-23T23:38:24Z

Hello @jonaspleyer, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

jonaspleyer · 2024-11-23T23:38:47Z

@editorialbot check repository

editorialbot · 2024-11-23T23:39:10Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.24 s (1283.6 files/s, 165768.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                           111           3077           5334          26564
Python                          17            367            185           2023
TOML                            30             68             11            545
Markdown                        11             96              0            474
SVG                              3              0              0            334
TeX                              1             25              0            333
Jupyter Notebook                 2              0            290            254
HTML                             3              1              4            185
YAML                            17             39              7            170
JSON                           115              0              0            115
Bourne Shell                     4             11              3             35
-------------------------------------------------------------------------------
SUM:                           314           3684           5834          31032
-------------------------------------------------------------------------------

Commit count by author:

  2530	Jonas Pleyer

editorialbot · 2024-11-23T23:39:14Z

Paper file info:

📄 Wordcount for paper.md is 2826

✅ The paper includes a Statement of need section

editorialbot · 2024-11-23T23:39:15Z

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

jonaspleyer · 2024-11-23T23:40:35Z

In addition, the branch with your paper does not seem to include the software as well, but only has the paper. Typically, the paper branch is the same as the main branch, with the addition of the paper. Can you fix this?

@danielskatz
I have updated the paper branch to also include the most recent version of cellular_raza. The editorialbot seems to pick up the corresponding information correctly.

danielskatz · 2024-11-23T23:46:11Z

@danielskatz Thanks for initiating the pre-review process. I was aware that my paper is longer than the expected maximum size. I am very happy to trim it down. Is it reasonable to make this decision via the review process or would you like me to make these changes before advancing?

You need to reduce it before we start.

jonaspleyer · 2024-11-23T23:53:50Z

Thanks for the quick reply. I will reduce it in the coming week.

jonaspleyer · 2024-11-25T08:20:08Z

@danielskatz It seems that the editorialbot has counted words which were commented out. I had left some previous sections in comments in the source code of the paper.md file in case we need access to this information. When removing these paragraphs, the total word-count is approximately half (1345 words)
It seems that only the source file paper.md is scanned which also includes the preamble and other commands that will be compiled (such as figures). Without checking, it seems that the wc utility of the GNU coreutils is being used. When accounting for some of these additional contributions and gradually reducing the file, we obtain the following table.

Removed via Compilation	Wordcount
Full	2826
Without Comments	1345
Without Preamble	1293
Without Figures	1266
Others
Without Headings	1220
Without inline Citations	1199
Without Acknowledgements	1160

It is clear that we are still over the desired 1000 words but much closer than thought initially. We will nevertheless try to compact the paper.

jonaspleyer · 2024-11-25T08:21:04Z

@editorialbot check repository

editorialbot · 2024-11-25T08:21:27Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.25 s (1247.2 files/s, 160213.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                           111           3077           5334          26564
Python                          17            367            185           2023
TOML                            30             68             11            545
SVG                              3              0              0            334
TeX                              1             25              0            333
Markdown                        11             55              0            302
Jupyter Notebook                 2              0            290            254
HTML                             3              1              4            185
YAML                            17             39              7            170
JSON                           115              0              0            115
Bourne Shell                     4             11              3             35
-------------------------------------------------------------------------------
SUM:                           314           3643           5834          30860
-------------------------------------------------------------------------------

Commit count by author:

  2531	Jonas Pleyer

editorialbot · 2024-11-25T08:21:31Z

Paper file info:

📄 Wordcount for paper.md is 1345

✅ The paper includes a Statement of need section

editorialbot · 2024-11-25T08:21:33Z

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

danielskatz · 2024-11-26T13:37:23Z

@editorialbot generate pdf

editorialbot · 2024-11-26T13:39:36Z

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

editorialbot · 2024-11-26T13:40:26Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

danielskatz · 2024-11-26T13:41:17Z

👋 @jonaspleyer - is this ready now from your point of view?

jonaspleyer · 2024-11-26T18:46:05Z

@editorialbot check repository

editorialbot · 2024-11-26T18:46:27Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.28 s (1112.4 files/s, 142846.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Rust                           111           3077           5334          26564
Python                          17            367            185           2023
TOML                            30             68             11            545
SVG                              3              0              0            334
TeX                              1             25              0            333
Markdown                        11             54              0            286
Jupyter Notebook                 2              0            290            254
HTML                             3              1              4            185
YAML                            17             39              7            170
JSON                           115              0              0            115
Bourne Shell                     4             11              3             35
-------------------------------------------------------------------------------
SUM:                           314           3642           5834          30844
-------------------------------------------------------------------------------

Commit count by author:

  2536	Jonas Pleyer

editorialbot · 2024-11-26T18:46:31Z

Paper file info:

📄 Wordcount for paper.md is 1159

✅ The paper includes a Statement of need section

editorialbot · 2024-11-26T18:46:32Z

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

jonaspleyer · 2024-11-26T18:48:37Z

👋 @jonaspleyer - is this ready now from your point of view?

Yes I would be happy to advance. 👍

danielskatz · 2024-11-26T18:51:17Z

@jonaspleyer - We've switched the track this is in, so @Kevin-Mattheus-Moerman will be handling it from here. Thanks for your work to get it ready to be assigned to an editor.

jonaspleyer · 2024-11-29T14:18:45Z

@Kevin-Mattheus-Moerman Just wanted to know if there is anything that I should do before we enter the review stage?

Kevin-Mattheus-Moerman · 2024-11-29T17:03:46Z

@editorialbot generate pdf

editorialbot · 2024-11-29T17:05:58Z

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

editorialbot · 2024-11-29T17:06:45Z

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Submitting author: @bramvandijk88
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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

jonaspleyer · 2024-12-05T14:47:11Z

@Kevin-Mattheus-Moerman Hi sorry to bother you again. Since this submission has changed tracks and Managing EiC, I would simpliy like to clarify if there is anything which I should do.

Kevin-Mattheus-Moerman · 2025-01-10T15:01:18Z

@jonaspleyer apologies for the delays encountered here so far. We have a big of a backlog of submissions to go through. As such many editors are per-occupied with other submissions. I will assign a handling editor as soon as one becomes available.

Kevin-Mattheus-Moerman · 2025-01-10T15:02:43Z

@editorialbot invite @mahfuz05062 as editor

editorialbot · 2025-01-10T15:02:46Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2025-01-10T15:03:04Z

@mahfuz05062 since one of your submissions is nearly done, do you think you can help edit this one? Thanks

mahfuz05062 · 2025-01-10T22:11:10Z

@editorialbot assign @mahfuz05062 as editor

editorialbot · 2025-01-10T22:11:13Z

Assigned! @mahfuz05062 is now the editor

mahfuz05062 · 2025-01-10T22:11:42Z

Hi @jonaspleyer, do you have any suggestions for potential reviewers? If so, please mention them here (without tagging them with an @). You can search the list of people who have already agreed to review and may be suitable for this submission. I will then reach out to the potential reviewers to finalize the reviewers for this submission.

jonaspleyer · 2025-01-16T10:24:16Z

Hi there! Thanks for advancing this submission and apologies for the slow response on my end.
I have looked at the list of people and found some names which might be suitable.

https://reviewers.joss.theoj.org/reviewers/5922
https://reviewers.joss.theoj.org/reviewers/3276
https://reviewers.joss.theoj.org/reviewers/3961
https://reviewers.joss.theoj.org/reviewers/2247

mahfuz05062 · 2025-01-18T22:24:18Z

Hi @Armavica, @finsberg, @johanneskoester, and @lazear - any of you interessted in reviewing this article?

finsberg · 2025-01-19T11:14:50Z

Hi @Armavica, @finsberg, @johanneskoester, and @lazear - any of you interessted in reviewing this article?

Hi @mahfuz05062, I would be happy to review this one👍

editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 23, 2024

editorialbot added TeX Shell labels Nov 23, 2024

danielskatz added the paused label Nov 24, 2024

editorialbot added Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials and removed Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 26, 2024

Kevin-Mattheus-Moerman added waitlisted Submissions in the JOSS backlog due to reduced service mode. and removed paused labels Jan 10, 2025

editorialbot assigned mahfuz05062 Jan 10, 2025

[PRE REVIEW]: cellular_raza: Cellular Agent-based Modeling from a Clean Slate #7520

[PRE REVIEW]: cellular_raza: Cellular Agent-based Modeling from a Clean Slate #7520

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