[REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6474

editorialbot · 2024-03-13T11:51:01Z

Submitting author: @sportiellomike (Mike Sportiello)
Repository: https://github.com/sportiellomike/mousebreedeR
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @csoneson
Reviewers: @yjunechoe, @jsun
Archive: 10.5281/zenodo.11405147

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/dcbcc4d1aac93c71fea9292eb0ef8ed5/status.svg)](https://joss.theoj.org/papers/dcbcc4d1aac93c71fea9292eb0ef8ed5)

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

@yjunechoe & @jsun, 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:

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✨ 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 @yjunechoe

📝 Checklist for @jsun

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

editorialbot · 2024-03-13T11:51:04Z

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editorialbot · 2024-03-13T11:51:18Z

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

OK DOIs

- 10.1210/endocr/bqaa114 is OK
- 10.1371/journal.pone.0012418 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-13T11:51:25Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (1908.7 files/s, 85596.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               20             65            400            374
Rmd                              1             30             79             89
Markdown                         3             26              0             52
TeX                              1              1              0             27
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            26            123            483            560
-------------------------------------------------------------------------------

Commit count by author:

    40	sportiellomike
    17	Mike Sportiello

editorialbot · 2024-03-13T11:51:31Z

Paper file info:

📄 Wordcount for paper.md is 738

✅ The paper includes a Statement of need section

editorialbot · 2024-03-13T11:51:34Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-03-13T11:52:06Z

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

csoneson · 2024-03-13T11:52:32Z

👋🏼 @sportiellomike, @yjunechoe, @jsun - this is the review thread for the submission. 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

yjunechoe · 2024-03-13T12:45:01Z

Review checklist for @yjunechoe

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/sportiellomike/mousebreedeR?
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 (@sportiellomike) 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).
- See [JOSS REVIEW] Example usage sportiellomike/mousebreedeR#2
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?
- See [JOSS REVIEW] Automated tests sportiellomike/mousebreedeR#1
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
- See [JOSS REVIEW] Community guidelines sportiellomike/mousebreedeR#3

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?

csoneson · 2024-03-26T19:24:51Z

👋🏻 Just wanted to check in to see that things were going well here and that there are no questions about the process (@jsun - I see that you haven't yet created your checklist, let me know if you have any questions!)
Thanks all!

yjunechoe · 2024-03-26T20:46:44Z

Hi @csoneson - I'm returning to this review after my first pass at the checklist (I have been awaiting a response from the author about automated tests before I proceed further)

I took some time to read the contents of this package more closely, and I have some serious concerns about the Substantial scholarly effort criterion.

Inside the package I count 12 functions - a combined LOC of 273 lines and an average of 23 lines for each function (LOC range: 4-45). Looking at internal function calls as a proxy for complexity, each function in the package is composed of an average 13 calls to other functions, mostly c(), return(), and print(). See below for the code involved in this analysis.

I'm afraid there's not much for me to work with here to evaluate the package. As per the review guidelines, I would like to flag the submission as questionable scope before proceeding further.

Analysis of substantial scholarly effort

## Setup
functions <- c(
  "addmouseID",
  "addpoints",
  "canwegetalltheallelesfromonecross",
  "compilegametes",
  "engageinmeiosis",
  "fertilize",
  "pointsperpup",
  "possiblepointsfromdesiredoutcome",
  "spermandeggs",
  "summarizefertilization",
  "summarizepotentialpups",
  "whichpairsshouldibreed"
)
length(functions)
#> [1] 12

endpoint <- "https://raw.githubusercontent.com/sportiellomike/mousebreedeR/main/R/"
files <- file.path(endpoint, paste0(functions, ".R"))
lines <- lapply(files, readLines)

## Code lines
count_code_lines <- function(x) {
  code <- grep("^(#|\\s*$)", x, invert = TRUE, value = TRUE)
  length(code)
}
all_code_lines <- sapply(lines, count_code_lines)
sum(all_code_lines)
#> [1] 273
mean(all_code_lines)
#> [1] 22.75
range(all_code_lines)
#> [1]  4 45

## Function complexity
parsed <- lapply(lines, \(x) parse(text = paste(x, collapse = "\n")))
parse_data <- do.call(rbind, lapply(parsed, getParseData))
function_calls <- parse_data |>
  subset(token == "SYMBOL_FUNCTION_CALL" & !text %in% functions) |>
  el("text") |>
  table()
head(sort(function_calls, decreasing = TRUE))
#> 
#>  which      c return  print subset length 
#>     18     13     12      9      8      7
sum(function_calls)
#> [1] 152
sum(function_calls)/length(functions)
#> [1] 12.66667

sportiellomike · 2024-03-26T23:05:39Z

Apologies @yjunechoe, I wasn't aware you were waiting on me. I was waiting for your full review to come back before working on your recommendations.
The package itself was created to solve a few problems: help users sacrifice fewer mice, get the needed genotypes for given experiments in fewer crosses to accelerate research, and do so in a convenient way usable with any number of loci not constricted to one genetic model or organism. I believe we have accomplished that goal. The vignette walks through how it achieves this goal, in my opinion. I can't speak to whether solving those problems meets the threshold of the journal, but I do believe the package achieves the goals it set out to solve.

yjunechoe · 2024-03-26T23:48:02Z

Hi @sportiellomike - thanks for the quick response, and I apologize for not being clear on the issue I opened on automated tests

To your points - I understand your perspective on the usefulness of the tool (albeit I've not fully evaluated this formally). I only mean to comment on the structure and contents of the package as an open source software developed for general consumption, according to the scope and standards of JOSS specifically. To clarify, I'm following the practice of previous reviewers who have raised issues of LOC and complexity as part of evaluating the substantial scholarly effort criterion (see similar issues).

I'm happy to complete the review and help with the review process up to a successful publication, but substantial scholarly effort is a rather tricky matter to resolve, especially if the package is already considered to be at a feature-complete state that addresses its goals. I only seek clarification from the editorial team - I apologize again for the interruption.

csoneson · 2024-03-27T07:59:36Z

@yjunechoe Thanks for voicing your concern. Let me bring this up with the broader editor team and get back to you.

csoneson · 2024-03-27T07:59:39Z

@editorialbot query scope

editorialbot · 2024-03-27T07:59:41Z

Submission flagged for editorial review.

jsun · 2024-03-28T17:46:30Z

Sorry for the delay. Ill finish my review for next week.

jsun · 2024-04-04T21:18:20Z

Review checklist for @jsun

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/sportiellomike/mousebreedeR?
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 (@sportiellomike) 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?

sportiellomike · 2024-04-11T13:49:05Z

@csoneson: the reviewer @yjunechoe encouraged me to comment here regarding the "substantial scholarly effort" guideline in the other thread.

While I understand it to be the case JOSS wants longer submissions, I wanted to be clear that this project was created for the purpose of solving specific problems: the unnecessary death of experimental animals by requiring fewer crosses and therefore animals used, as well as increasing the speed of which experimentalists can obtain their desired animal of correct genotype. As a result, i believe this submission to be a substantial contribution as it has achieved those goals. It is true it is a smaller package, but it still is a large contribution to the field of experimental animal morbidity/mortality reduction, of which there is minimal resources, and no software resources that are free and open source to my knowledge. I am glad I was able to achieve these goals in a moderate number of lines of code instead of a large number as it is more efficient, though I freely admit this package is smaller than most published in JOSS. I hope you agree.

jsun · 2024-04-12T02:51:53Z

This package contains simple but important features to assist wet researchers. Therefore, I think, the main target users of this package would be wet researchers who are unfamiliar with coding programmes. Therefore, I recommend the author to create easy-to-use functions and clear documentation (vignette). The following comments are based on a check of this contribution.

package
- The function names in this package are long and difficult to read. If possible, please rename the function names (e.g.,summarizepotentialpups to summarize_potential_pups or summarizePotentialPups). Alternatively, please consider using the S4 class to develop this package. In this case, instead of using summarizepotentialpups, a simple summary function can be defined.
- If visualisation is one of the core features of this package, implement a plot function to reduce end-user costs.
- Please consider changing the output format of canwegetalltheallelesfromonecross and whichpairsshouldibreed functions. These outputs are not R-like.
vignette
- Many researchers who are not familiar with R do not know how to obtain vignettes, so please indicate how to obtain vignettes in README.md (perhaps after the 'How to install' section).
- Please add an 'Abstract' to the vignette to explain why this package is needed (which may overlap with the 'state of need' in the manuscript) and what this vignette describes.
- The figures in the vignette are too small to check. Please adjust the size of the figure (e.g., set the width to 100%).
- The vignette contains plot<-ggplot(subsetmelt)+geom_col(aes(y=percent,x=genotype,fill=genotype))+facet_wrap(~gene)+ kind of code. The plot is the famous generic function, please consider using other variable name to assign the ggplot object.
- Coding rules are not uniform. For example, whichpairstobreed<-whichpairsshouldibreed(x=pointsperpupoutput,desiredvector = desiredvec); there is no spaces between = and other contains the spaces.
- Some variable names are too long to catch the information. Please consider use shorter one or undanstandable one (e.g., compilegametesoutput to compilegametes_output)

csoneson · 2024-04-15T06:45:21Z

@csoneson: the reviewer @yjunechoe encouraged me to comment here regarding the "substantial scholarly effort" guideline in the other thread.

Thanks @sportiellomike - the editorial team is discussing the submission and we should have an answer for you soon! Thanks for your patience.

csoneson · 2024-04-16T09:41:53Z

Thank you for your patience, and thanks again @yjunechoe for raising the point about the scope. The editorial team has carefully reviewed the submission and the discussion, and we felt that although it is close to borderline, we would consider it in scope, and it seems to provide useful functionality for the target audience. Thus, I would encourage the reviewers to continue their evaluation of the submission. Thanks!

yjunechoe · 2024-04-16T11:38:15Z

@csoneson Thanks for the clarification!

@sportiellomike Apologies again for the interruption. I'll complete the rest of my review swiftly.

editorialbot · 2024-05-30T21:00:34Z

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

csoneson · 2024-05-31T06:58:23Z

Great, thanks - I'll make a new post below describing the next steps.

csoneson · 2024-05-31T06:58:26Z

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

sportiellomike · 2024-05-31T19:55:07Z

DONE: Double check authors and affiliations (including ORCIDs)

DONE (Version number is v1.0.0): 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.

DONE (DOI: [10.5281/zenodo.11405146](https://zenodo.org/doi/10.5281/zenodo.11405146)): Archive the release on Zenodo/figshare/etc and post the DOI here.

DONE: Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

DONE: Make sure that the license listed for the archive is the same as the software license.

sportiellomike · 2024-05-31T19:57:46Z

@csoneson I think we're all set here on my end! See above comment for doi etc.

10.5281/zenodo.11405146

csoneson · 2024-06-02T05:51:27Z

Thanks. Could you please edit the metadata of the Zenodo archive so that the title agrees with that of the paper? Also the format of the last author's name is slightly different (with/without the middle 'J').

Also one thing that I noticed only now - the GitHub repo and the LICENSE.md file gives the license as MIT; however, the License field in the DESCRIPTION file says 'CC BY 4.0'. Could you please change the latter to also be MIT?

sportiellomike · 2024-06-02T10:43:36Z

Title changed
J appropriately added to author
Description file now reflects correct license of MIT consistent with rest of package.

Sorry i missed those things @csoneson.

csoneson · 2024-06-02T14:27:06Z

@editorialbot set 10.5281/zenodo.11405147 as archive

editorialbot · 2024-06-02T14:27:08Z

Done! archive is now 10.5281/zenodo.11405147

csoneson · 2024-06-02T14:27:35Z

@editorialbot set v1.0.0 as version

editorialbot · 2024-06-02T14:27:38Z

Done! version is now v1.0.0

csoneson · 2024-06-02T14:28:04Z

Thanks - this looks good to me, I will hand off to the topic AEiC for the last steps. Thanks for submitting to JOSS!

csoneson · 2024-06-02T14:28:07Z

@editorialbot recommend-accept

editorialbot · 2024-06-02T14:28:09Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-06-02T14:28:23Z

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

OK DOIs

- 10.1210/endocr/bqaa114 is OK
- 10.1371/journal.pone.0012418 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-06-02T14:29:21Z

👋 @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#5435, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-06-04T12:50:50Z

@sportiellomike as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Everything appears in order so I will now continue to accept this work in JOSS.

Kevin-Mattheus-Moerman · 2024-06-04T12:50:57Z

@editorialbot accept

editorialbot · 2024-06-04T12:50:59Z

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

editorialbot · 2024-06-04T12:57:27Z

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: Sportiello
  given-names: Mike
  orcid: "https://orcid.org/0000-0003-1690-8702"
- family-names: Topham
  given-names: David J.
  orcid: "https://orcid.org/0000-0002-9435-8673"
contact:
- family-names: Sportiello
  given-names: Mike
  orcid: "https://orcid.org/0000-0003-1690-8702"
doi: 10.5281/zenodo.11405147
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sportiello
    given-names: Mike
    orcid: "https://orcid.org/0000-0003-1690-8702"
  - family-names: Topham
    given-names: David J.
    orcid: "https://orcid.org/0000-0002-9435-8673"
  date-published: 2024-06-04
  doi: 10.21105/joss.06474
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6474
  title: "MousebreedeR: A novel software to assist in the design of
    breeding schema for complex genotypes of experimental organisms"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06474"
  volume: 9
title: "MousebreedeR: A novel software to assist in the design of
  breeding schema for complex genotypes of experimental organisms"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-06-04T12:57:30Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-06-04T12:57:31Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06474 joss-papers#5448
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06474
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-06-05T07:11:48Z

@sportiellomike congratulations on this JOSS publication! 🎉

At this point I would like to thank @csoneson for editing this submission!

And a special thank you also to the reviewers: @yjunechoe, @jsun !!!!

editorialbot · 2024-06-05T07:11:49Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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  <img src="https://joss.theoj.org/papers/10.21105/joss.06474/status.svg" alt="DOI badge" >
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   :target: https://doi.org/10.21105/joss.06474

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editorialbot added R review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Mar 13, 2024

editorialbot assigned csoneson Mar 13, 2024

editorialbot mentioned this issue Mar 13, 2024

[PRE REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6214

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editorialbot added the query-scope Submissions of uncertain scope for JOSS label Mar 27, 2024

csoneson removed the query-scope Submissions of uncertain scope for JOSS label Apr 16, 2024

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 2, 2024

editorialbot added accepted published Papers published in JOSS labels Jun 4, 2024

Kevin-Mattheus-Moerman closed this as completed Jun 5, 2024

editorialbot mentioned this issue Oct 20, 2024

[PRE REVIEW]: Gene-based scientific literature visualiser (GeSciLiVis): an R package for interrogating published literature for experimentally-derived gene lists within a priori user-defined biological context #7376

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editorialbot mentioned this issue Nov 12, 2024

[PRE REVIEW]: simla-ts: A web application simulator for local anesthetic agents used in education of pharmacology written by Typescript #7461

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[REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6474

[REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6474

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editorialbot commented Mar 13, 2024 • edited Loading

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Review checklist for @yjunechoe

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Review checklist for @jsun

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Documentation

Software paper

sportiellomike commented Apr 11, 2024

jsun commented Apr 12, 2024

csoneson commented Apr 15, 2024

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