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

[whedon]

Submitting author: @taoliu032 (Tao Liu)
Repository: https://github.com/siminegroup/E2EDNA2
Version: v1.0
Editor: @csoneson
Reviewers: @JoaoRodrigues, @rvhonorato
Managing EiC: Kevin M. Moerman

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Author instructions

Thanks for submitting your paper to JOSS @taoliu032. Currently, there isn't an JOSS editor assigned to your paper.

@taoliu032 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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[whedon]

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

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[whedon]

PDF failed to compile for issue #4116 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.24 s (238.0 files/s, 67327.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              9              0              0           7642
Python                          36           1410           1607           4910
Markdown                         8             70              0            182
YAML                             1              1              0            172
Bourne Shell                     3             26             15             90
-------------------------------------------------------------------------------
SUM:                            57           1507           1622          12996
-------------------------------------------------------------------------------


Statistical information for the repository 'f841f8a3fe7a1563639de96d' was
gathered on 2022/02/01.
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           82.90
Tao Liu                         70          2448           1945           14.49
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          5.5                4.65
InfluenceFunctional        6252           38.8          3.8                9.77
Tao Liu                    1546           63.2          2.2               22.45

[taoliu032]

@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 📄 👈

[Kevin-Mattheus-Moerman]

@whedon invite @will-rowe as editor

[whedon]

@will-rowe has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@taoliu032 I have just waitlisted this submission since none of the editors in the bioinformatics domain are currently available. We will assign an editor once one becomes available.

[Kevin-Mattheus-Moerman]

@whedon invite @csoneson as editor

@csoneson do you think you'd be able to help edit this submission?

[whedon]

@csoneson has been invited to edit this submission.

[taoliu032]

@Kevin-Mattheus-Moerman Thank you very much! I was just wondering today if I should follow up :)

[csoneson]

👋🏻 @taoliu032 - I had a quick look at the submission, and I was wondering if you could perhaps quickly clarify a couple of things before we move on:

• The relation to E2EDNA (repo, paper) - admittedly this is not really my field of expertise, but it wasn't totally clear to me. The paper mentions that E2EDNA 2.0 is more user-friendly and easier to install, but it wasn't obvious if there are other significant additions/advantages/differences, and whether you would recommend E2EDNA users to switch to E2EDNA 2.0, or if they are to some extent complementary and you plan to maintain both going forward (the paper denotes them as predecessor/successor, but I couldn't see e.g. a note in the E2EDNA repo pointing people to E2EDNA 2.0).
• I see only instructions for installation on macOS, and a file macos_installation.sh in the repo - do you expect it to work also for other operating systems, or is there an inherent restriction to macOS? I suspect the provided environment yml file will not be portable.

Thanks!

[taoliu032]

Hello @csoneson - Thank you very much for questions!

• E2EDNA 2.0 relies on another molecular dynamics simulation engine (called "OpenMM") therefore avoids the difficult Tinker installation which is required in E2EDNA. Meanwhile, E2EDNA 2.0 offers 8 pre-coded user-friendly modes of simulations which E2EDNA does not offer. Currently, the two version are complementary in some aspect. Therefore, going forward we indeed intend to maintain both versions separately.
• Instructions for installation have been polished for macOS only for review purposes but we have this code installed and running on a Linux cluster - there are no inherent limitations on the OS. For review purposes we focused on ironing out the issues for a particular system.

Thank you! Feel free to let us know if there are other questions :D 😁

[csoneson]

@whedon assign @csoneson as editor

[whedon]

OK, the editor is @csoneson

[csoneson]

@taoliu032 Thanks! I'll start by looking for a couple of suitable reviewers for this submission - if you have any suggestions (e.g. from the list in the first comment above), feel free to mention them here.

[csoneson]

👋🏻 @ayush9pandey, @ayaanhossain - would you be interested in reviewing this submission for JOSS?

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands

[ayush9pandey]

I don't think I have the right expertise to be a reviewer for this submission, so I'll pass.

[taoliu032]

@csoneson thank you so much!
After going through the list looking for reviewers in computational chemistry/molecular dynamics simulation particularly, here are two suggestions: JoaoRodrigues and rvhonorato - both are GitHub handles. However, I do not know about either of them and there are so many experts under the same categories. Therefore, feel free to select any reviewers as you see fit :) Have a wonderful week!

[csoneson]

@ayush9pandey - no problem, thanks for responding!

[csoneson]

👋🏻 @JoaoRodrigues, @rvhonorato - would you be interested in reviewing this submission for JOSS?

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands

[rvhonorato]

Thanks for the invite @csoneson and for the suggestion @taoliu032.

Yes I'd like to review this one!

[csoneson]

Brilliant, thanks @rvhonorato! Once we have one more reviewer we'll start the actual review issue where you'll have your checklist etc.

[taoliu032]

@csoneson May I ask to slightly modify the code? One of the toggles was not perfectly set up but it does not affect the backbone or main features of the code at all. I literally just need to edit one line and delete a few.

This is my first ever submission to JOSS (very exciting experience!), so I am not sure if I could make changes to the code at the moment or if I should wait till the official review starts to bring up this request. I wonder if you could point out what action would be deemed to be most appropriate?

My apologies for any inconvenience! Thank you very much!

[csoneson]

@taoliu032 - yes, feel free to go ahead and make this change. Once the review has started, it may be good to refrain from making major changes at the very same time that the reviewers are going through the code, just because it may become very confusing which version should be checked :)

[taoliu032]

@csoneson Thank you for clarification! I have just made the change to the JOSS branch. Yes exactly, I do not intend to confuse any reviewers therefore the JOSS branch will become off limits once the review starts 🙂

[csoneson]

Pinging @JoaoRodrigues and @ayaanhossain - would one of you be interested in reviewing this submission for JOSS?

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands

[JoaoRodrigues]

Hi @csoneson, happy to review. Sorry for the delay in replying!

[csoneson]

Thank you @JoaoRodrigues! With two reviewers on board, I'm gonna start the review issue, I'll provide more information over there.

[csoneson]

@whedon assign @JoaoRodrigues as reviewer

[whedon]

OK, @JoaoRodrigues is now a reviewer

[csoneson]

@whedon add @rvhonorato as reviewer

[whedon]

OK, @rvhonorato is now a reviewer

[csoneson]

@whedon start review

[whedon]

OK, I've started the review over in #4182.