[REVIEW]: E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands

[whedon]

Submitting author: @taoliu032 (Tao Liu)
Repository: https://github.com/siminegroup/E2EDNA2
Branch with paper.md (empty if default branch): JOSS
Version: v2.0.0
Editor: @csoneson
Reviewers: @JoaoRodrigues, @rvhonorato
Archive: 10.5281/zenodo.6546661

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Review checklist for @JoaoRodrigues

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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 (@taoliu032) 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

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?
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• 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 @rvhonorato

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@taoliu032) 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

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 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. @JoaoRodrigues, @rvhonorato it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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To fix this do the following two things:

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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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[whedon]

PDF failed to compile for issue #4182 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.20 s (288.0 files/s, 81482.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              9              0              0           7642
Python                          36           1410           1616           4901
Markdown                         8             70              0            182
YAML                             1              1              0            172
Bourne Shell                     3             26             15             90
-------------------------------------------------------------------------------
SUM:                            57           1507           1631          12987
-------------------------------------------------------------------------------


Statistical information for the repository '9b4b94e70467b97ea0b4cd3b' was
gathered on 2022/02/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
ISDementyev                     95           486            303            2.60
InfluenceFunctional             30         16125           9003           82.84
Tao Liu                         71          2458           1955           14.55
siminegroup                      1             1              1            0.01

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
ISDementyev                 129           26.5          5.9                4.65
InfluenceFunctional        6252           38.8          4.1                9.77
Tao Liu                    1546           62.9          2.6               23.03

[csoneson]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

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

[csoneson]

👋🏼 @taoliu032, @JoaoRodrigues, @rvhonorato - this is the review thread for the submission. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread. As you go over the submission, please check any items that you feel have been satisfied. There are also 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.

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

[taoliu032]

Thank you all very much! To both reviewers: feel free to ask me any questions about the manuscript and software in any way as you see fit :)

Wish everyone a wonderful weekend :D

[rvhonorato]

This code might have a licensing issue, but since i am not a licensing expert, I will raise the point here for discussion:

I have noticed in your installation instructions the following:

params['ld setup path'], params['ld run path'], etc: paths to various LightDock Python scripts, providing they are in a working directory. No need to change these paths. The paths are used to automatically copy the scripts to ld_scripts/ within a working directory from lib/lightdock/.

Which then, as expected results in the lightdock scripts being copied from the lightdock package and in your execution.

To my understanding the fact the the script are being copied rather than imported the lightdock from the library makes necessary for your code to also be GPLv3, whereas it is now Apache-2.

Since you are just using the scripts and not modifying them (as far as I know) it is better to import the scripts and use then from within your code to avoid any issues.

Ping brianjimenez (lightdock creator) and also @JoaoRodrigues (the other reviewer) since they might also have some insights into this.

[brianjimenez]

Thanks for the ping @rvhonorato
Indeed, it could be a license conflict here since redistributing code with a different license than LightDock (GPLv3) might not be allowed (but needs a double check for Apache-2 + GPLv3 compatibility). If authors are not modifying the code, simpler could be just to add LightDock as a pip dependency and those scripts would be available in the path.

[taoliu032]

@rvhonorato Thank you so much for raising the concern! We are not very experienced in choosing a license for open source software -- I was in fact planning to consult JOSS reviewers on the choice of license :) But certainly we do not want to have any licensing conflict.

@brianjimenez Thank you for helping out! We got the scripts from https://github.com/lightdock/lightdock/tree/0.9.2/bin and we did include LightDock package using pip when creating a conda virtual environment; Otherwise, those scripts would not run either.
I will try the direct import for the methods in those scripts. One (probably unnecessary) concern is that: when I looked at the "lightdock" folder under "site-packages" in the conda environment, I did not see those scripts. I will check the LightDock documentation to figure out how to do the import properly. If you can point out any direction or document, it would be super helpful too. Thank you again!

[brianjimenez]

Hi @taoliu032 , glad to help! To find LightDock scripts, I assume you use virtualenv command (conda should behave in a similar way):

virtualenv venv
source venv/bin/activate
pip install lightdock

After installation ends, you should find LightDock scripts on venv/bin folder. Try also which ant_thony.py to locate scripts. When the virtual environment (or conda) is activated, all LightDock scripts are available at any path.

Hope it helps!

[taoliu032]

@brianjimenez - I removed the commands of copying individual lightdock scripts and our code can still run successfully. Thank you for the suggestion!

@rvhonorato - After removing the script-copying commands, I have tested the code both on my local macOS machine and our Linux-based computer cluster (the job waited in the queue for a while). Both tests ran successfully and I have also pushed the updates to the JOSS branch :-) Please feel free to download the new code - sorry for causing any inconvenience! Let me know if there is any other concern or questions, thank you!

[csoneson]

👋🏻 Hi all - just wanted to check in how things are going here - let me know if you have any questions!

[JoaoRodrigues]

EDIT:

I just realized I should have opened an issue in the target repo with my comments. I just did and copied the comments there. The link to the issue is here.

[taoliu032]

@JoaoRodrigues Thank you for the comments! Our responses have been added to the same issue.

[csoneson]

👋🏻 @JoaoRodrigues - did you have a chance to take a look at @taoliu032's responses to your review?
@rvhonorato - could you update us on how your review is progressing?

Thanks all!

[csoneson]

Ping @JoaoRodrigues, @rvhonorato - could you update us on how things are progressing here? Thanks!

[rvhonorato]

Sorry for the delay, I'll take a look at this asap!

[csoneson]

@JoaoRodrigues, @rvhonorato - any updates here?

[JoaoRodrigues]

Hi @csoneson, apologies, I haven't had as much time to work on this as I wanted. Replied to the authors just now. Last thing I would need before 👍 is to test the software locally. Unfortunately, the current examples (AFAIK) require some third-party software that I'd have to register to download, and I don't want to do so. I've asked the authors to provide an example that does not require those modules, since they've mentioned that that is a possibility.

[taoliu032]

Thank you for the comment. An example has been prepared as requested, please see the detail here: siminegroup/E2EDNA2#14 (comment).

As always, please do not hesitate to ping me should there be any question.

[rvhonorato]

@JoaoRodrigues did most of the heavy lifting pointing at most of the points I had with the code, thanks ;) For me before the final OK I also just need to test it locally, going over it now based on the link by @taoliu032 above.

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1021/acs.jcim.1c00696 is OK
- 10.3390/cancers10030080 is OK
- 10.1007/s11302-020-09733-y is OK
- 10.1089/nat.2021.0085 is OK
- 10.1016/j.omtn.2019.10.042 is OK
- 10.1007/978-1-0716-1803-5_25 is OK
- 10.3390/biomedicines6020053 is OK
- 10.1002/jcc.21596 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1093/bioinformatics/btx555 is OK
- 10.1093/bioinformatics/btz642 is OK
- 10.1109/TCBB.2010.104 is OK
- 10.1093/bioinformatics/btv545 is OK
- 10.1093/bioinformatics/btz897 is OK
- 10.2174/138161212799958477 is OK
- 10.1038/nrd.2016.199 is OK
- 10.1126/science.2200121 is OK
- 10.1039/b618909a is OK
- 10.1021/ac049858n is OK
- 10.3389/fchem.2020.00434 is OK
- 10.1021/acsnano.6b02558 is OK
- 10.3390/bios8020054 is OK
- 10.1007/s12038-020-0017-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'maxLength'] The value has a length of '35'; this exceeds the allowed maximum length of '17'.

[tarleb]

Huh 😕

Sorry about that, I'll look into it again.

[csoneson]

Thanks @tarleb! Looks like the same fix may need to be applied to the ISBN field 🙂

[tarleb]

OK, applied the fix to that field as well. Should work now. 🤞

[csoneson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1021/acs.jcim.1c00696 is OK
- 10.3390/cancers10030080 is OK
- 10.1007/s11302-020-09733-y is OK
- 10.1089/nat.2021.0085 is OK
- 10.1016/j.omtn.2019.10.042 is OK
- 10.1007/978-1-0716-1803-5_25 is OK
- 10.3390/biomedicines6020053 is OK
- 10.1002/jcc.21596 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1093/bioinformatics/btx555 is OK
- 10.1093/bioinformatics/btz642 is OK
- 10.1109/TCBB.2010.104 is OK
- 10.1093/bioinformatics/btv545 is OK
- 10.1093/bioinformatics/btz897 is OK
- 10.2174/138161212799958477 is OK
- 10.1038/nrd.2016.199 is OK
- 10.1126/science.2200121 is OK
- 10.1039/b618909a is OK
- 10.1021/ac049858n is OK
- 10.3389/fchem.2020.00434 is OK
- 10.1021/acsnano.6b02558 is OK
- 10.3390/bios8020054 is OK
- 10.1007/s12038-020-0017-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3243

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3243, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[csoneson]

Yay! Thanks for the fix @tarleb

[csoneson]

@taoliu032 This will now go to the associate editor-in-chief on rotation for the last steps. Thanks for your patience!

[taoliu032]

Hooray! Thank you @csoneson and thank you for the fix @tarleb

[danielskatz]

@taoliu032 - I'm the AEiC this week, and have a few small changes for the paper: please merge siminegroup/E2EDNA2#20 or let me know what you disagree with, then we can proceed to publication.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1021/acs.jcim.1c00696 is OK
- 10.3390/cancers10030080 is OK
- 10.1007/s11302-020-09733-y is OK
- 10.1089/nat.2021.0085 is OK
- 10.1016/j.omtn.2019.10.042 is OK
- 10.1007/978-1-0716-1803-5_25 is OK
- 10.3390/biomedicines6020053 is OK
- 10.1002/jcc.21596 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1093/bioinformatics/btx555 is OK
- 10.1093/bioinformatics/btz642 is OK
- 10.1109/TCBB.2010.104 is OK
- 10.1093/bioinformatics/btv545 is OK
- 10.1093/bioinformatics/btz897 is OK
- 10.2174/138161212799958477 is OK
- 10.1038/nrd.2016.199 is OK
- 10.1126/science.2200121 is OK
- 10.1039/b618909a is OK
- 10.1021/ac049858n is OK
- 10.3389/fchem.2020.00434 is OK
- 10.1021/acsnano.6b02558 is OK
- 10.3390/bios8020054 is OK
- 10.1007/s12038-020-0017-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3245

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3245, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.04182 joss-papers#3246
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04182
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...

[danielskatz]

Congratulations to @taoliu032 (Tao Liu) and co-authors!!

And thanks to @JoaoRodrigues and @rvhonorato for reviewing, and @csoneson for editing!
We couldn't do this without you

[editorialbot]

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

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[taoliu032]

Thank you to all of you for your time and help!