[REVIEW]: Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates #6293

editorialbot · 2024-01-28T19:05:01Z

Submitting author: @moritzobenauer (Moritz Obenauer)
Repository: https://github.com/moritzobenauer/ProjectRaccoon
Branch with paper.md (empty if default branch):
Version: v1.0.2
Editor: @jromanowska
Reviewers: @taoliu032, @lorenzo-rovigatti
Archive: 10.5281/zenodo.10776652

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/a72d0ea4ef2c43b6384a5fff784aa1ba/status.svg)](https://joss.theoj.org/papers/a72d0ea4ef2c43b6384a5fff784aa1ba)

Reviewers and authors:

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Reviewer instructions & questions

@taoliu032 & @lorenzo-rovigatti, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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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 @taoliu032

📝 Checklist for @lorenzo-rovigatti

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

editorialbot · 2024-01-28T19:05:04Z

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

For a list of things I can do to help you, just type:

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

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editorialbot · 2024-01-28T19:05:05Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (638.0 files/s, 89691.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             1              0              0           1683
Python                          21            468            325           1465
YAML                             5             22             12            147
Markdown                         4             52              0            127
TeX                              1              9              0            117
Bourne Shell                     1             11              7             41
Jupyter Notebook                 1              0            267             27
-------------------------------------------------------------------------------
SUM:                            34            562            611           3607
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-01-28T19:05:07Z

Wordcount for paper.md is 805

editorialbot · 2024-01-28T19:05:18Z

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

OK DOIs

- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jctc.9b00054 is OK
- 10.1080/08927022.2010.507247 is OK
- 10.1002/marc.201800459 is OK
- 10.1146/annurev-chembioeng-092319-083243 is OK
- 10.1002/jcc.20945 is OK
- 10.54677/MNMH8546 is OK
- 10.1186/1758-2946-4-17 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-28T19:06:23Z

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

jromanowska · 2024-01-28T19:08:22Z

👋🏼 @moritzobenauer @taoliu032 @lorenzo-rovigatti, this is the review thread for the paper. All of our communications will happen here from now on.

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

@editorialbot generate my checklist

as the top of a new comment in this thread.

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

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

taoliu032 · 2024-01-29T03:14:08Z

Review checklist for @taoliu032

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/moritzobenauer/ProjectRaccoon?
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 (@moritzobenauer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

Documentation

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

Software paper

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

lorenzo-rovigatti · 2024-01-29T09:26:20Z

Review checklist for @lorenzo-rovigatti

Conflict of interest

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

Code of Conduct

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

General checks

Repository: Is the source code for this software available at the https://github.com/moritzobenauer/ProjectRaccoon?
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 (@moritzobenauer) 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?

taoliu032 · 2024-02-04T16:05:13Z

@moritzobenauer Hi Moritz, firstly thanks for putting together such a package! Before getting into the paper and codebase, I want to clarify what seems like a small issue in the list of authors. In the article proof, one author is tagged with *, indicating co-authorship. I guess at least one more author should also be labeled with * ?

moritzobenauer · 2024-02-04T17:08:30Z

@moritzobenauer Hi Moritz, firstly thanks for putting together such a package! Before getting into the paper and codebase, I want to clarify what seems like a small issue in the list of authors. In the article proof, one author is tagged with *, indicating co-authorship. I guess at least one more author should also be labeled with * ?

Hey taoliu032,

You're absolutely right. I thought my corresponding authorship would imply an equal contribution. I updated the paper. Thank you for the hint and sorry for the oversight.

jromanowska · 2024-02-19T07:49:37Z

👋 @lorenzo-rovigatti , @taoliu032 - how is the review process going? It has been 3 weeks since the process started, so I just wanted to check on you.

Let me know if you are able to complete the review process and how long time do you need.

taoliu032 · 2024-02-21T14:04:54Z

Hi @jromanowska thanks for checking in! I crossed out some items on the to-do list and will continue to do more this weekend :) I plan to fully go through the list by next weekend (or sooner).

lorenzo-rovigatti · 2024-02-22T09:00:42Z

Hey @jromanowska ! I have started my review process (as you can see from the issue above, which was promptly solved). I hope I'll be done by the weekend.

lorenzo-rovigatti · 2024-02-23T14:36:29Z

First of all, thanks to @moritzobenauer (and the other authors) for this nice piece of software. I have added three issues to the repo, with one of them which has been already closed.

While the authors work on the the other issues, I have a couple of comments on some specific items that can be more easily discussed here:

According to the commit history, the code has been authored by @moritzobenauer and @kainszs . Did the other authors contribute to the code in some other ways?
Community guidelines (see the checklist above) are missing.

kainszs · 2024-02-24T10:00:07Z

Hi,
we have noticed that with increasingly larger sequences, we get performance issues when generating the polymer.

We are testing the module against the example sequence. We have noticed that the actions sometimes abort due to a runtime error, i.e. that the tests exceed the 6h limit. This is the case with almost every fourth test.

You can run the tests via

python -m unittest

I attribute this to the fact that the generation of the sequence by the self-avoiding-random walk is in a continuous loop because no displacement vector is found that fulfills the minimum distance condition.

The polymer is generated in project_raccoon/src/functions/standard.py using the functions 'generate_file() and get_semi_random_walk_shift(). We store all coordinates of the polymer in a matrix and generate a vector $\vec{k}$ so that the coordinates of the new monomer buildingblock added with $\vec{k}$ exceed at least the threshold as distance. Do you have any idea how we can fix this without increasing the threshold? We would be grateful for any ideas.

@lorenzo-rovigatti @taoliu032

taoliu032 · 2024-02-26T04:12:59Z

I had some comments on the documentation and testing as well, and have added to the already opened issue above. Hope they are helpful!

Following [this discussion](moritzobenauer#11), linked to the [JOSS review](openjournals/joss-reviews#6293), this is a commit showing an example of how to strengthen the parsing of the sequence file by raising exceptions containing why and where the parsing fails.

lorenzo-rovigatti · 2024-02-26T12:44:11Z

Hi, we have noticed that with increasingly larger sequences, we get performance issues when generating the polymer.

We are testing the module against the example sequence. We have noticed that the actions sometimes abort due to a runtime error, i.e. that the tests exceed the 6h limit. This is the case with almost every fourth test.

You can run the tests via
python -m unittest
I attribute this to the fact that the generation of the sequence by the self-avoiding-random walk is in a continuous loop because no displacement vector is found that fulfills the minimum distance condition.

The polymer is generated in project_raccoon/src/functions/standard.py using the functions 'generate_file() and get_semi_random_walk_shift(). We store all coordinates of the polymer in a matrix and generate a vector k→ so that the coordinates of the new monomer buildingblock added with k→ exceed at least the threshold as distance. Do you have any idea how we can fix this without increasing the threshold? We would be grateful for any ideas.

@lorenzo-rovigatti @taoliu032

I'm not familiar with the inner workings of the code, but I have written codes to generate my fair share of polymer configurations before, and what is perhaps happening here is that sometimes the code gets "trapped" in a configuration where the $k+1$-th monomer cannot be possibly added for geometrical reasons. As a result, the code gets stuck and runs forever. If I were you, I'd add a check that makes the code re-generate the chain from scratch if a monomer is added $N$ times without success. I'm not sure what $N$ should be, but something like $10^3$, $10^4$ looks like a sensible choice.

kainszs · 2024-02-27T07:47:31Z

That works outrageously well. Thank you @lorenzo-rovigatti

jromanowska · 2024-03-06T08:13:03Z

@moritzobenauer - I've noticed that one of the references lacks a DOI (https://onlinelibrary.wiley.com/doi/10.1002/0471721204.ch8) - could you fix that and re-create the PDF?

moritzobenauer · 2024-03-06T08:34:23Z

@editorialbot check references

editorialbot · 2024-03-06T08:34:41Z

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

OK DOIs

- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jctc.9b00054 is OK
- 10.1080/08927022.2010.507247 is OK
- 10.1002/marc.201800459 is OK
- 10.1146/annurev-chembioeng-092319-083243 is OK
- 10.1002/jcc.20945 is OK
- 10.54677/MNMH8546 is OK
- 10.1002/0471721204.ch8 is OK
- 10.1186/1758-2946-4-17 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/1593511 is INVALID

moritzobenauer · 2024-03-06T08:41:51Z

@editorialbot check references

editorialbot · 2024-03-06T08:42:33Z

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

OK DOIs

- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jctc.9b00054 is OK
- 10.1080/08927022.2010.507247 is OK
- 10.1002/marc.201800459 is OK
- 10.1146/annurev-chembioeng-092319-083243 is OK
- 10.1002/jcc.20945 is OK
- 10.54677/MNMH8546 is OK
- 10.1002/0471721204.ch8 is OK
- 10.1186/1758-2946-4-17 is OK

MISSING DOIs

- None

INVALID DOIs

- None

moritzobenauer · 2024-03-06T08:43:17Z

I added the DOI @jromanowska and checked the references.

jromanowska · 2024-03-08T08:48:52Z

@editorialbot generate pdf

editorialbot · 2024-03-08T08:49:59Z

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

jromanowska · 2024-03-08T08:52:56Z

@editorialbot set 10.5281/zenodo.10776652 as archive

editorialbot · 2024-03-08T08:52:57Z

Done! archive is now 10.5281/zenodo.10776652

jromanowska · 2024-03-08T08:53:32Z

@editorialbot set v1.0.2 as version

editorialbot · 2024-03-08T08:53:34Z

Done! version is now v1.0.2

jromanowska · 2024-03-08T08:54:33Z

@editorialbot recommend-accept

editorialbot · 2024-03-08T08:54:35Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-08T08:54:51Z

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

OK DOIs

- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jctc.9b00054 is OK
- 10.1080/08927022.2010.507247 is OK
- 10.1002/marc.201800459 is OK
- 10.1146/annurev-chembioeng-092319-083243 is OK
- 10.1002/jcc.20945 is OK
- 10.54677/MNMH8546 is OK
- 10.1002/0471721204.ch8 is OK
- 10.1186/1758-2946-4-17 is OK

MISSING DOIs

- No DOI given, and none found for title: Python 3 Reference Manual

INVALID DOIs

- None

editorialbot · 2024-03-08T08:56:14Z

👋 @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#5103, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jromanowska · 2024-03-08T08:57:53Z

@lorenzo-rovigatti @taoliu032 @moritzobenauer @kainszs - thank you all once more. I've read the paper once more and checked the meta data on zenodo. One of the Chief Editors will now go through all and if all's fine, we will accept the paper.

The proofs has just been generated, so you may always double-check it and write in the comment here if you noticed any mistakes.

Kevin-Mattheus-Moerman · 2024-03-10T08:22:40Z

@moritzobenauer I have checked your paper, this archive, your repository, and the archive link. Most seems in order. I only have the below points that require your attention:

Please edit the author order for the archive to match the paper author order.
Please edit the archive listed version tag to match v1.0.2 it currently says 1.0.2.
Looking at your repository I do not see a clear link to any contributing guidelines. Would you be able to add a simple CONTRIBUTING.md file and link to it from the README.md? This website features some templates: https://contributing.md/example/

moritzobenauer · 2024-03-10T09:00:35Z

Hello @Kevin-Mattheus-Moerman ,

I worked on your suggestions:

[ x] Please edit the author order for the archive to match the paper author order.

Order is now MLO, KNS, PB, and FS matching the paper.

[ x] Please edit the archive listed version tag to match v1.0.2 it currently says 1.0.2.

Version tag is set to v1.0.2.

[x ] Looking at your repository I do not see a clear link to any contributing guidelines. Would you be able to add a simple CONTRIBUTING.md file and link to it from the README.md? This website features some templates: contributing.md/example

Added contributing.md and codeofconduct.md to the project and created a link in the README.md under 'Supported Building Blocks' where we explain contributions to the project.

Kevin-Mattheus-Moerman · 2024-03-10T12:26:28Z

@editorialbot accept

editorialbot · 2024-03-10T12:26:30Z

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

editorialbot · 2024-03-10T12:33:00Z

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: Obenauer
  given-names: Moritz L.
  orcid: "https://orcid.org/0009-0003-8140-9907"
- family-names: Spauszus
  given-names: Kai N.
  orcid: "https://orcid.org/0009-0006-0650-2273"
- family-names: Besenius
  given-names: Pol
  orcid: "https://orcid.org/0000-0001-7478-4459"
- family-names: Schmid
  given-names: Friederike
  orcid: "https://orcid.org/0000-0002-5536-6718"
contact:
- family-names: Obenauer
  given-names: Moritz L.
  orcid: "https://orcid.org/0009-0003-8140-9907"
doi: 10.5281/zenodo.10776652
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Obenauer
    given-names: Moritz L.
    orcid: "https://orcid.org/0009-0003-8140-9907"
  - family-names: Spauszus
    given-names: Kai N.
    orcid: "https://orcid.org/0009-0006-0650-2273"
  - family-names: Besenius
    given-names: Pol
    orcid: "https://orcid.org/0000-0001-7478-4459"
  - family-names: Schmid
    given-names: Friederike
    orcid: "https://orcid.org/0000-0002-5536-6718"
  date-published: 2024-03-10
  doi: 10.21105/joss.06293
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6293
  title: "Project RACCOON: Automated construction of PDB files for
    polymers and polymer peptide conjugates"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06293"
  volume: 9
title: "Project RACCOON: Automated construction of PDB files for
  polymers and polymer peptide conjugates"

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 · 2024-03-10T12:33:03Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-10T12:33:04Z

🚨🚨🚨 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.06293 joss-papers#5114
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06293
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

moritzobenauer · 2024-03-10T13:23:52Z

Everything looks great to me. Thank you @lorenzo-rovigatti , @taoliu032 , and @jromanowska for the smooth reviewing process.

editorialbot · 2024-03-12T10:21:46Z

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

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06293/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06293/status.svg
   :target: https://doi.org/10.21105/joss.06293

This is how it will look in your documentation:

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editorialbot added Jupyter Notebook Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jan 28, 2024

editorialbot assigned jromanowska Jan 28, 2024

editorialbot mentioned this issue Jan 28, 2024

[PRE REVIEW]: Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates #6219

Closed

lorenzo-rovigatti mentioned this issue Feb 21, 2024

Can't run the suggested example moritzobenauer/ProjectRaccoon#10

Closed

This was referenced Feb 23, 2024

JOSS review: sanitising the sequence file moritzobenauer/ProjectRaccoon#11

Closed

JOSS review: documentation & testing moritzobenauer/ProjectRaccoon#12

Closed

lorenzo-rovigatti mentioned this issue Feb 26, 2024

Strengthen the parsing of the sequence file moritzobenauer/ProjectRaccoon#13

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 8, 2024

editorialbot added accepted published Papers published in JOSS labels Mar 10, 2024

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[REVIEW]: Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates #6293

[REVIEW]: Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates #6293

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