[REVIEW]: NORDic: a Network-Oriented package for the Repurposing of Drugs

[editorialbot]

Submitting author: !--author-handle-->@clreda<!--end-author-handle-- (Clémence Réda) Repository: https://github.com/clreda/NORDic Branch with paper.md (empty if default branch): Version: v2.4.4 Editor: !--editor-->@lpantano<!--end-editor-- Reviewers: @cauliyang, @sevgisu0227 Archive: 10.5281/zenodo.8355529

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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

@cauliyang & @sevgisu0227, 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 @lpantano 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 @cauliyang

📝 Checklist for @sevgisu0227

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (278.2 files/s, 326117.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            421           1321           4276
Jupyter Notebook                10              0          48360            907
TeX                              1             37              0            389
Markdown                         2             62              0            181
YAML                             4             15              0            159
JSON                             3              0              0             72
ASP                              1              1              0             58
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            48            536          49681           6045
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2118

[editorialbot]

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

OK DOIs

- 10.1172/JCI66220 is OK
- 10.1038/nrm2503 is OK
- 10.1016/0022-5193(74)90172-6 is OK
- 10.1016/0022-5193(69)90015-0 is OK
- 10.48550/arXiv.2212.12756 is OK
- 10.1038/s41598-020-73147-4 is OK
- 10.1038/s41467-018-06008-4 is OK
- 10.1038/npjsba.2016.15 is OK
- 10.1093/cid/ciab350 is OK
- 10.1073/pnas.1610622114 is OK
- 10.1016/j.cell.2008.09.050 is OK
- 10.1073/pnas.1533293100 is OK
- 10.48550/arXiv.2111.01479 is OK
- 10.1007/978-3-031-15034-0_5 is OK
- 10.1186/s13059-016-1097-7 is OK
- 10.1186/1471-2105-7-S1-S7 is OK
- 10.1093/bioinformatics/btr274 is OK
- 10.1109/ictai.2019.00014 is OK
- 10.1038/npjsba.2016.10 is OK
- 10.1371/journal.pcbi.1007900 is OK
- 10.1093/bioinformatics/btq124 is OK
- 10.1038/npjsba.2016.20 is OK
- 10.1093/bioinformatics/btaa484 is OK
- 10.48550/arXiv.2103.10070 is OK
- 10.1371/journal.pone.0044459 is OK
- 10.1101/gr.1239303 is OK
- 10.1093/bioinformatics/btx764 is OK
- 10.1093/bioinformatics/btv305 is OK
- 10.1038/s41598-019-54180-4 is OK
- 10.1145/956750.956769 is OK
- 10.1101/2020.05.27.119016 is OK
- 10.1016/j.cell.2017.10.049 is OK
- 10.1038/nmeth.4077 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gkaa1074 is OK
- 10.1093/bib/bbw112 is OK
- 10.5281/zenodo.7239047 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[cauliyang]

Review checklist for @cauliyang

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/clreda/NORDic?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@clreda) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[lpantano]

Hi @cauliyang, @sevgisu0227, just wondering how this was going? do you think you can finish up this in the next 2 weeks? Thanks!

[cauliyang]

Hi @lpantano, Sorry for the delay, and I can finish that in the next 2 weeks.

[cauliyang]

My Current Comments

1. Installation

• pip install NORDic failed on macOS arm64

  ERROR: Failed building wheel for pyeda

• conda install -c colomoto -y -q maboss failed on macOS arm64

  The following package could not be installed
  └─ maboss does not exist (perhaps a typo or a missing channel).

• conda install -c creda -y -q nordic failed on macOS arm64.

  The following package could not be installed
  └─ nordic is not installable because it requires
  └─ bonesis >=0.4.91 , which does not exist (perhaps a missing channel).

I recommend adding all dependencies in your package's meta.yaml so that users do not need to install dependencies themselves. That is pro of conda as well. Then submit the package to Bioconda or conda channel instead of your personal channel.

Claim the platform the package will support (e.g. Linux, windows, macOS)

[clreda]

Hello @cauliyang, thanks for reviewing this package!

Could you please detail the error in building the wheel when using pip? (was it in a virtual environment, using conda or virtualenv, etc. Have you got wheel in that environment? otherwise perhaps you should run python3 -m pip install wheel which I will add to the README). The dependencies mentioned in the README (maboss, graphviz, etc.) are already in the meta.yaml file. However, these packages are not available on PyPI, hence the installation lines.

Did you test pip installation first, or did you try installing maboss first?

Noted for the platforms, as I have mainly tried (and made people try) on Linux. I will check the requirements for submitting to conda or Bioconda.

[cauliyang]

Hi @clreda , I figured it out finally, the problem is thanks to the package pyeda.
The package NORDic can be installed via pip and conda successfully. But the readme may be confusing. we do not need to install dependencies if we install via conda. It is better to clarify when we need to install dependencies ourselves in the installation information.

Reproducibility

it seems like the file you use in the notebook does not exist. for example ToyOndine/inferred_maximal_solution.png in NORDic Network Simulations.ipynb

Test

The test looks a little bit messy, and it is better to use pytest or unittest to manage all your tests.

Others

• use a formatter (e.g black) can make code more clean and readable
• follow https://peps.python.org/pep-0008/ or https://google.github.io/styleguide/pyguide.html will be better

[sevgisu0227]

Review checklist for @sevgisu0227

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/clreda/NORDic?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@clreda) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[clreda]

@cauliyang I am glad to hear that the problem is solved! I have corrected the README to include the differences between the installation with PyPI and Conda.

About your reproducibility concern: the notebooks are supposed to be run in a given order. Indeed, most of the notebooks rely on the network inferred in notebook NORDic CoLoMoTo.ipynb, as the inference code might be a bit too large to add to every notebook. I will clarify this dependency in all notebooks.

I will reformat the testing code to use unittest as suggested. I will check out formatter Black and the guidelines you have mentioned, thank you!

[lpantano]

@cauliyang , this the last replied solve your last question about reproducibility? @sevgisu0227, do you think you can finish this in the next week or post the issues you are having? Thanks!

[cauliyang]

@lpantano, the explanation of reproducibility makes sense but the automated tests may still require some effort.

[sevgisu0227]

@lpantano sorry for the delay, I will finish it this week.

[sevgisu0227]

Installation worked fine, I used pip install option and manually installed the dependencies both on Mac OS and Ubuntu 20.04 LTS. One recommendation would be to include recommended minimum system requirements.

Functionality documentation

I am non academic user, so this may be specific to me, I had to ask someone else for lincs sign-up. providing an alternative, ie. downloading the files from clue which does not require sign-up and processing it could be more helpful. For reproducibility and version control purposes, I would provide these databases as reference files and avoid API access all together.

providing a summary of recommended (or potentially default) parameters, adding usage function for the parameters and short descriptions would make it a lot more user friendly.

[clreda]

Dear @cauliyang I have rewritten the automated tests in the package using unittest. Please let me know if it is better to you

Dear @sevgisu0227 thank you for accepting to review this paper. The main issue I see with providing the database could be space-consuming for most of them (ex. LINCS and STRING, in several dozens of GB). Using the API version of the database also ensures that the query results are up to date and do not manually require me to monitor all the databases and redownload them at each update. As an answer to your reproducibility problem, I can possibly suggest writing down the date of creation of the model, which can be connected to the latest version at that date of each database. I will add further documentation in the docstrings in the next weeks, including short descriptions, usage examples, and default/recommended values.

[cauliyang]

@clreda, appreciate your effort. Now the project looks alright but I recommend sharing the notebook via colab or others. That is very continent for users to give the tool a try without bothering with environment configuration. Besides, using examples as documentation is acceptable but not perfect. If we have another concise API documentation, which is neat.

[clreda]

Dear @cauliyang I have found that using directly the CoLoMoTo docker might answer the concern of users wishing to avoid environment configuration issues, as it includes the first tutorial notebook in NORDic. I have specified how to use it in the README as well as in the documentation website. This documentation website might answer your second concern, about concise API documentation. I have also tackled one of your earliest concerns about submitting to a larger conda channel. I chose bioconda (see pull request). I hope to have everything fixed in the next weeks.

Dear @sevgisu0227 I have added further documentation in the docstrings, with short descriptions and default/recommended values (please refer to the documentation website). I haven't added the usage examples, because since most of the arguments in functions rely on custom structures introduced in NORDic, showcasing NORDic functionalities through notebooks might make those functions easier to use that long docstring descriptions.

Please let me know if you have other concerns.

[cauliyang]

Hi @clreda, Thanks for your effort and consideration! A Docker environment is also a better alternative. Bioconda is a wise choice and promotes the tool to the larger community. The document systems are on the right track as well. In summary, your changes resolve my concerns. Keep the library alive and friendly!

[clreda]

Dear @cauliyang thanks a lot for your feedback, which allows NORDic to be more accessible and useful to the community!

[lpantano]

@sevgisu0227, are the last changes address you final missing items in the checklist? I think we are only waiting for those one to finish the review.thanks!

[sevgisu0227]

@lpantano Yes everything looks good, great documentation.

[clreda]

Dear @sevgisu0227 thank you very much for your feedback that improved the user experience with NORDic!

[lpantano]

@editorialbot generate pdf

[lpantano]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1172/JCI66220 is OK
- 10.1038/nrm2503 is OK
- 10.1016/0022-5193(74)90172-6 is OK
- 10.1016/0022-5193(69)90015-0 is OK
- 10.48550/arXiv.2212.12756 is OK
- 10.1038/s41598-020-73147-4 is OK
- 10.1038/s41467-018-06008-4 is OK
- 10.1038/npjsba.2016.15 is OK
- 10.1093/cid/ciab350 is OK
- 10.1073/pnas.1610622114 is OK
- 10.1016/j.cell.2008.09.050 is OK
- 10.1073/pnas.1533293100 is OK
- 10.48550/arXiv.2111.01479 is OK
- 10.1007/978-3-031-15034-0_5 is OK
- 10.1186/s13059-016-1097-7 is OK
- 10.1186/1471-2105-7-S1-S7 is OK
- 10.1093/bioinformatics/btr274 is OK
- 10.1109/ictai.2019.00014 is OK
- 10.1038/npjsba.2016.10 is OK
- 10.1371/journal.pcbi.1007900 is OK
- 10.1093/bioinformatics/btq124 is OK
- 10.1038/npjsba.2016.20 is OK
- 10.1093/bioinformatics/btaa484 is OK
- 10.48550/arXiv.2103.10070 is OK
- 10.1371/journal.pone.0044459 is OK
- 10.1101/gr.1239303 is OK
- 10.1093/bioinformatics/btx764 is OK
- 10.1093/bioinformatics/btv305 is OK
- 10.1038/s41598-019-54180-4 is OK
- 10.1145/956750.956769 is OK
- 10.1101/2020.05.27.119016 is OK
- 10.1016/j.cell.2017.10.049 is OK
- 10.1038/nmeth.4077 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gkaa1074 is OK
- 10.1093/bib/bbw112 is OK
- 10.5281/zenodo.7239047 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[lpantano]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] 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.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

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

[clreda]

The latest release version on GitHub is v2.4.4. The DOI of the corresponding Zenodo release is 10.5281/zenodo.8355529.

[clreda]

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] 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.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] Make sure that the license listed for the archive is the same as the software license.

[lpantano]

@editorialbot set v2.4.4 as version

[editorialbot]

Done! version is now v2.4.4

[lpantano]

@clreda, thank you for the information. Can you make the tittle to be exactly the same in the paper and in Zenodo? Thanks!

[clreda]

@clreda, thank you for the information. Can you make the tittle to be exactly the same in the paper and in Zenodo? Thanks!

Done! Thanks a lot for your work!

[lpantano]

Thank you! I have been reading the paper again, and I think we should reduce the information on it to be around 1500 words, no counting references. Right now the text contains more than 2000 words (can you check that?). If that is true, I am thinking about the following: 1-reduce introduction to half a page. 2-For these sections: Automated identification of disease-related Boolean networks and Prioritization of master regulators in Boolean networks, there first couple of paragraphs is about the current work and issues to solve. I think this is very important and I will keep this information in the documentation for instance, but maybe in the paper, it would be good to focus last part of the section that explain NORDic implementation and try to summarize in one paragraph the issues.

Maybe the current information can be in the docs (if they are not yet there), and the paper can be shorter. I know it is a lot of work to explain the current status of the field and the good things NORDic is bringing.

Let me know if you think is possible to bring the text to ~1500 words. Thanks in advance.

[clreda]

@editorialbot generate pdf

[clreda]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/nrm2503 is OK
- 10.1016/0022-5193(74)90172-6 is OK
- 10.1016/0022-5193(69)90015-0 is OK
- 10.48550/arXiv.2212.12756 is OK
- 10.1038/s41598-020-73147-4 is OK
- 10.1073/pnas.1610622114 is OK
- 10.1016/j.cell.2008.09.050 is OK
- 10.1073/pnas.1533293100 is OK
- 10.48550/arXiv.2111.01479 is OK
- 10.1007/978-3-031-15034-0_5 is OK
- 10.1371/journal.pcbi.1007900 is OK
- 10.48550/arXiv.2103.10070 is OK
- 10.1093/bioinformatics/btx764 is OK
- 10.1093/bioinformatics/btv305 is OK
- 10.1038/s41598-019-54180-4 is OK
- 10.1145/956750.956769 is OK
- 10.1101/2020.05.27.119016 is OK
- 10.1016/j.cell.2017.10.049 is OK
- 10.1038/nmeth.4077 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gkaa1074 is OK
- 10.5281/zenodo.7239047 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[clreda]

Dear @lpantano please find in the previous message the reduced version of the paper, which I believe is less than 1,500 words now. I have removed the references which are no longer present in the paper, and posted the full version of the paper in the documentation: https://clreda.github.io/NORDic/paper.html

Let me know if that solves your concerns.

[lpantano]

@editorialbot set up archive as 10.5281/zenodo.8355529

[editorialbot]

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

@editorialbot commands

[lpantano]

@editorialbot set archive as 10.5281/zenodo.8355529

[editorialbot]

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

@editorialbot commands

[lpantano]

@editorialbot set 10.5281/zenodo.8355529 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8355529

[lpantano]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...