search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
707 stars 37 forks source link

[REVIEW]: Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD #1698

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @tonigi (Toni Giorgino) Repository: https://github.com/giorginolab/vmd_diffusion_coefficient Version: v1.2 Editor: @labarba Reviewer: @jrperilla, @HaoZeke Archive: 10.5281/zenodo.3445530

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/25d51faf73cc17ae3affb51b787bbe18"><img src="https://joss.theoj.org/papers/25d51faf73cc17ae3affb51b787bbe18/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/25d51faf73cc17ae3affb51b787bbe18/status.svg)](https://joss.theoj.org/papers/25d51faf73cc17ae3affb51b787bbe18)

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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @labarba know.

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

Review checklist for @jrperilla

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @HaoZeke

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 5 years ago

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

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

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

@whedon generate pdf
whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

labarba commented 5 years ago

👋 @jrperilla, @HaoZeke — Thank you for agreeing to review this submission for JOSS. At the top of this Review issue, each of you has a review checklist: work your way through it, and post any questions or comments for the authors here. You can also open new issues in the submission repository, linking to this thread here for a cross-reference. Godspeed!

HaoZeke commented 5 years ago

Thanks @labarba. Right, so, off the bat, @tonigi, the LICENSE file has issues, essentially, it is currently not an OSI approved license. I am opening an issue in the repo to discuss this further.

tonigi commented 5 years ago

Thanks for spotting it! Updated LICENSE to the BSD-3 text.

HaoZeke commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- 10.1016/0263-7855(96)00018-5 is OK
- 10.1042/BJ20130960 is OK
- 10.1038/srep19839 is OK
- 10.33011/livecoms.1.1.5068 is OK
- 10.1016/S0006-3495(02)73971-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None
tonigi commented 5 years ago

@HaoZeke made amendments according to suggestions. Also, regarding the "Functionality" point, added an explanation of the demo calculation and how the results compare with experimental ones. :)

HaoZeke commented 5 years ago

@tonigi Thanks for the very prompt resolution of all points raised. @labarba I am pleased to say that I have completed my review, and recommend this for publication.

labarba commented 5 years ago

@jrperilla — May I ask for an update on your review?

jrperilla commented 5 years ago

The Diffusion Coefficient Tool in VMD offers a simple and accessible method to glean diffusion coefficients from mean square displacement of a molecular species within a molecular dynamics trajectory. Given that diffusion coefficients computed from MD data can help to validate equilibration or otherwise detect the presence of bulk motions, this software is of particular interest to the computational chemistry community. To test the method appropriately, i.e., following guidelines stated by the author in the JOSS manuscript, an equilibrated system was chosen describing roughly 30,000 TIP3P waters over 4 microseconds. While the plugin functioned as intended and produced consistent results given different values of stride and lag intervals, from both command-line and GUI, some concerns regarding the structure and design of the tool were noted during testing.

  1. Auto_path variable issue
  2. Crash during initialization
  3. Output the diffusion coefficient from linear fit to stdout

Minor issues or feature requests:

  1. Spelling and typos
  2. Killswitch request
  3. Print the equivalent command-line arguments to stdout
  4. Printout functionality
tonigi commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tonigi commented 5 years ago

@jrperilla Thanks for the suggestions! Each item is answered in the corresponding issue. In short, all the added functionality now constitutes release 1.2. The paper and docs are updated accordingly.

jrperilla commented 5 years ago

I think all my concerns were addressed and the paper is ready for publication.

jrperilla commented 5 years ago

I want to shout out to @abryer94 for helping with the testing of the code.

labarba commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- 10.1016/0263-7855(96)00018-5 is OK
- 10.1042/BJ20130960 is OK
- 10.1038/srep19839 is OK
- 10.33011/livecoms.1.1.5068 is OK
- 10.1016/S0006-3495(02)73971-4 is OK
- 10.1093/bioinformatics/btu037 is OK

MISSING DOIs

- None

INVALID DOIs

- None
labarba commented 5 years ago

@whedon set v1.2 as version

whedon commented 5 years ago

OK. v1.2 is the version.

labarba commented 5 years ago

@tonigi — We're now going to need you to make an archive deposit in Zenodo (or a similar service) get a DOI, and post the DOI here.

Please edit the archive metadata so the title and author list matches the JOSS paper.

tonigi commented 5 years ago

Hi @labarba , just tried with Zenodo's GitHub integration and got ...

DOI

10.5281/zenodo.3445530

tonigi commented 5 years ago

@HaoZeke , @jrperilla , @abryer94 -- thanks for the thorough reviews!

@labarba -- thanks for managing!

Sorry for the nitpicking - I just wanted to point out that non-ascii "ff" combined characters slipped in the title. I guess it's better to rename them to plain "ff" before submission lest we hit some "undocumented feature" in the next steps such as cross-ref indexing etc.

labarba commented 5 years ago

@whedon set 10.5281/zenodo.3445530 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3445530 is the archive.

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/968

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/968, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
labarba commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/969
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01698
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

labarba commented 5 years ago

Congratulations, @tonigi, your JOSS paper is now published! 🚀

Huge thanks to our reviewers: @jrperilla, @HaoZeke — your contribution to JOSS is very much appreciated! 🙏

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.01698/status.svg)](https://doi.org/10.21105/joss.01698)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01698">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01698/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01698/status.svg
   :target: https://doi.org/10.21105/joss.01698

This is how it will look in your documentation:

DOI

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: