[REVIEW]: graphsim: An R package for simulating gene expression data from graph structures of biological pathways

[whedon]

Submitting author: @TomKellyGenetics (S. Thomas Kelly)
Repository: https://github.com/TomKellyGenetics/graphsim
Version: v1.0.0-joss
Editor: @majensen
Reviewer: @rcannood, @corybrunson
Archive: 10.5281/zenodo.3931288

Status

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Reviewers and authors:

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Reviewer instructions & questions

@rcannood & @corybrunson, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @rcannood

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@TomKellyGenetics) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @corybrunson

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@TomKellyGenetics) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @rcannood, @corybrunson it looks like you're currently assigned to review this paper 🎉.

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Reference check summary:

OK DOIs

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- 10.1016/S1357-4310(99)01461-6 is OK
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- 10.1016/j.ddtec.2013.12.002 is OK
- 10.1038/nrg3899 is OK
- 10.1016/j.cell.2015.11.015 is OK
- 10.1186/gb-2004-5-10-r80 is OK

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- https://doi.org/10.1038/nrg1272 may be missing for title: Network biology: understanding the cell’s functional organization
- https://doi.org/10.1038/nrg2918 may be missing for title: Network medicine: a network-based approach to human disease
- https://doi.org/10.1093/bib/bbr012 may be missing for title: Travelling the world of gene–gene interactions
- https://doi.org/10.1016/s0306-4379(97)00021-5 may be missing for title: A New and Versatile Method for Association Generation
- https://doi.org/10.1111/j.2517-6161.1995.tb02031.x may be missing for title: Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
- https://doi.org/10.1093/biostatistics/kxj037 may be missing for title: Adjusting batch effects in microarray expression data using empirical Bayes methods
- https://doi.org/10.1038/nrc1691 may be missing for title: The concept of synthetic lethality in the context of anticancer therapy
- https://doi.org/10.1186/gm99 may be missing for title: Synthetic Lethality: a framework for the development of wiser cancer therapeutics
- https://doi.org/10.1371/journal.pone.0125795 may be missing for title: Predicting human genetic interactions from cancer genome evolution
- https://doi.org/10.1002/emmm.201100150 may be missing for title: Combined genomic and phenotype screening reveals secretory factor SPINK1 as an invasion and survival factor associated with patient prognosis in breast cancer
- https://doi.org/10.1158/1535-7163.mct-14-1092 may be missing for title: Synthetic lethal screens identify vulnerabilities in GPCR signalling and cytoskeletal organization in E-cadherin-deficient cells
- https://doi.org/10.1016/j.neo.2014.04.007 may be missing for title: CSNK1E/CTNNB1 are synthetic lethal to TP53 in colorectal cancer and are markers for prognosis
- https://doi.org/10.1186/1755-8794-6-30 may be missing for title: Identification of potential synthetic lethal genes to p53 using a computational biology approach
- https://doi.org/10.1093/nar/gkv007 may be missing for title: limma powers differential expression analyses for RNA-sequencing and microarray studies
- https://doi.org/10.1083/jcb.200212033 may be missing for title: Adhesion-independent mechanism for suppression of tumor cell invasion by E-cadherin
- https://doi.org/10.1002/j.1460-2075.1995.tb00301.x may be missing for title: E-cadherin is a tumour/invasion suppressor gene mutated in human lobular breast cancers
- https://doi.org/10.1016/j.ccr.2014.08.008 may be missing for title: DAISY: Picking Synthetic Lethals from Cancer Genomes
- https://doi.org/10.1038/bjc.1997.523 may be missing for title: E-cadherin inactivation in lobular carcinoma in situ of the breast: an early event in tumorigenesis
- https://doi.org/10.1101/cshperspect.a003129 may be missing for title: Involvement of Members of the Cadherin Superfamily in Cancer
- https://doi.org/10.1002/(sici)1096-9896(199712)183:4<404::aid-path1148>3.0.co;2-9 may be missing for title: Simultaneous loss of E-cadherin and catenins in invasive lobular breast cancer and lobular carcinoma in situ
- https://doi.org/10.1038/nrc2620 may be missing for title: Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits

INVALID DOIs

- None

[majensen]

Replicating @arfon comment here regarding trimming bibtex entries:

@TomKellyGenetics - you might want to truncate your bibtex entries to only those that are cited in the JOSS paper to prevent Whedon responses like this one: #2137 (comment)

#2137 (comment)

[majensen]

@TomKellyGenetics - in the first paragraph of Methodology and software, there is a sentence:

...of the popular package, which is often used...

Seems like the package name is missing here, or I'm missing something.

[TomKellyGenetics]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[TomKellyGenetics]

This should build with updates from minor (formatting) corrections from errors found while submitting to CRAN and bioRxiv. I’ll look into removing unneeded references from the bibtex file. An updated submission with corrected documentation has been re-uploaded to CRAN and is pending manual confirmation.

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[TomKellyGenetics]

Dear Arfon,

Thank you for informing us on your policy. I'm currently based in Japan (which is considering to declare a state of emergency) so we're acutely aware of the developing situation here. I understand completely if reviews will take longer than usual during this time. I am safely able to work from home so can still respond to reviewers if they are able to.

Thank you,

Tom Kelly, Postdoctoral researcher at RIKEN IMS, Yokohama

[corybrunson]

@TomKellyGenetics the submission looks pretty cool, as i'm just starting my review. I have some comments on the paper before i begin exploring the software. Sorry if you've already caught some of these but not yet updated the PDF.

• I think "Present address:" should be removed from the second affiliation (RIKEN).
• On my reading, the abstract-style Statement of Need encapsulates what graphsim does but doesn't really justify it. This is taken care of in the Summary, so could the Statement of Need be excised? I know JOSS guidelines require a statement of need, but in my experience this does not need to be a separate section. (@majensen this is something i've wondered before. Does JOSS prefer the SoN to be a section with header?)
• The paper could use a careful proofreading. For example, there is a stray curly brace after "R" in the Summary, and "released as the package" would read more clearly as "released as a package".
• In the first paragraph of "Methodology and software", it's not clear to me whether the simulation procedure you've implemented is of your own design or is already widely used but not yet conveniently packaged. If it is the same procedure as that of Wang &al (2018), then it would be good to say this at the start.
• Package names are not showing up in the paper.
• The section cross-reference at the end of "Generating a Simulated Expression Dataset" is broken.

[corybrunson]

@TomKellyGenetics a couple of other comments, specifically on the code in the paper:

• The gplots package is used but not explicitly attached to the library.
• There's at least one typo: trace = "none\" toward the bottom of page 6.
• I'm unable to exactly reproduce the heatmaps displayed in the paper. They're based on the graph with inhibitions, and i'm also not clear on how to incorporate the vector state into these calculations, after looking into the code only a slight bit. (For issues running examples, etc. in the package itself, i'll open issues on the GitHub repo.)

[corybrunson]

@TomKellyGenetics one last point on the paper:

• The second author has not directly contributed to the package, as reflected on GitHub. Could you briefly describe their contributions to the project in the paper?

[rcannood]

Sorry for my late response, I didn't manage to find any spare time until now. @majensen I wanted to start the review just now, but I see I missed the opportunity to accept whedon's invitation to the repository. (I thought I had retained the rights since my previous review, but apparently they get removed after the review is done.) Could I somehow be invited again?

[TomKellyGenetics]

Thanks @corybrunson, I'll take a look at Issues as they come into the package repo (I think the problem with plot_directed is resolved).

I can reformat the Statement of Need if this is required explicitly by JOSS. I made it a separate section (as done by other recent submissions) so it would be clear for the editorial process.

Sorry it seems that some text formatting for language and package names weren't handled well when exporting LaTeX to whedon-compatible markdown. I've fixed these on the biorXiv version and I'll update the JOSS submission accordingly.

Wang et al (2018) also simulate gene expression counts as a log-normal distribution. This package was originally developed before this publication. The approach to simulate based on graph structures is our original design. To my knowledge, there are no pre-existing implementations for this procedure in R.

The second author is my PhD supervisor. He was involved in planning, overseeing the project and preparing the manuscript. He has tested the software and given feedback on it.

I'll update the PDF once I've corrected the issues mentioned with the markdown document.

[arfon]

@whedon re-invite @rcannood

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[arfon]

@whedon re-invite @rcannood as reviewer

[whedon]

OK, the reviewer has been re-invited.

@rcannood please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[rcannood]

Thanks @arfon @whedon!

[majensen]

Thanks @arfon; WB @rcannood !

[majensen]

@corybrunson - my opinion as editor (which will be addressed by @arfon if I'm wrong) is that the paper should be sure to include the rationale for writing the software and why there is a niche for it. Not necessary to have a heading (personally, I think that would be stylistically gauche-- but that's only my opinion!).

[corybrunson]

@TomKellyGenetics no problem, i'll come back to the PDF after the next update.

Regarding the Statement of Need, i'll be fine with the current formatting (above the Summary with its own header) if you want to keep it (thank you @majensen for your comment); my concern is that it says only what the software does, not what need it satisfies. The first three paragraphs of the Introduction do this quite well, so i'd suggest encapsulating them into 2 or 3 sentences for that purpose.

Onward to the software itself. : )

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1550

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1550, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[TomKellyGenetics]

@majensen Thanks, I agree to this change so I've pushed a correction.

i.e., "studies, as well as bulk...".

I think I've got this in time to be compiled in the final submission.

[majensen]

@openjournals/joss-eics We are ready to recommend this work for acceptance. Thanks!

[kyleniemeyer]

Hi @TomKellyGenetics, before accepting I found just a few things in the paper to fix:

• typo in third sentence: "uesad" -> "used"
• the limma reference has a a typo in the bib file, I think there is a space missing between a comma and and causing a problem:

{Matthew E R., and Phipson, B.,and Wu, D.,  and Hu, Y.,  and Law, C.W.,  and Shi, W., and Smyth, G.K.,}

should be

{Matthew E R., and Phipson, B., and Wu, D., and Hu, Y., and Law, C.W., and Shi, W., and Smyth, G.K.,}

[TomKellyGenetics]

Thanks for letting me know @kyleniemeyer, the corrected version should be pushed now.

[TomKellyGenetics]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kyleniemeyer]

@TomKellyGenetics looks good!

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1038/nrg1272 is OK
- 10.1093/nar/gkt1102 is OK
- 10.1007/978-3-642-01689-9 is OK
- 10.3389/fgene.2019.00535 is OK
- 10.1093/imanum/22.3.329 is OK
- 10.1093/bioinformatics/btm639 is OK
- 10.1038/nrg.2016.87 is OK
- 10.3892/ijo.2012.1744 is OK
- 10.1186/gb-2014-15-2-r29 is OK
- 10.1186/s12859-015-0778-7 is OK
- 10.1186/1471-2105-8-s6-s5 is OK
- 10.1093/nar/gkv007 is OK
- 10.1038/nprot.2017.149 is OK
- 10.1038/nrg2934 is OK
- 10.1101/2020.02.06.936971 is OK
- 10.1101/716811 is OK
- 10.1186/1752-0509-3-41 is OK
- 10.1101/227033 is OK
- 10.1109/msp.2007.273053 is OK
- 10.1186/s13059-017-1305-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1551

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1551, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02161 joss-papers#1552
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02161
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congrats @TomKellyGenetics on your article's publication in JOSS!

Many thanks to @rcannood and @corybrunson for reviewing, and @majensen for editing.

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02161/status.svg)](https://doi.org/10.21105/joss.02161)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02161">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02161/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02161/status.svg
   :target: https://doi.org/10.21105/joss.02161

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[majensen]

Really nice paper @TomKellyGenetics - @corybrunson and @rcannood I appreciate your huge contribution during these strange days. Hope you will all think of JOSS next time you publish!
--@majensen

[TomKellyGenetics]

Thanks again, @majensen @corybrunson and @rcannood, I'm very impressed by the JOSS review process. This a great initiative for the open-source community. I have put my name in the hat to review. 😊