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[REVIEW]: dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets #6129

Closed editorialbot closed 3 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@WillHannon-MCB<!--end-author-handle-- (William Hannon) Repository: https://github.com/dms-viz/dms-viz.github.io Branch with paper.md (empty if default branch): submit-joss-manuscript Version: v0.8.5 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @afrubin, @jkanche Archive: 10.5281/zenodo.12693853

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Markdown: [![status](https://joss.theoj.org/papers/205a2d1c7edb1e197975de88091f3073/status.svg)](https://joss.theoj.org/papers/205a2d1c7edb1e197975de88091f3073)

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

@afrubin & @jkanche, 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 @csoneson 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 @jkanche

📝 Checklist for @afrubin

editorialbot commented 10 months ago

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:

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (269.0 files/s, 96391.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                       8            292            495           2781
JSON                             3              0              0           2337
TeX                              2             22             25            751
CSS                              1             73              3            462
HTML                             2              2             23            402
Markdown                         5            231              0            286
YAML                             2              7              7             44
-------------------------------------------------------------------------------
SUM:                            23            627            553           7063
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/ve/vead055 is OK
- 10.1101/2020.10.29.339317 is OK
- 10.1016/j.cell.2023.02.001 is OK
- 10.21105/joss.02353 is OK
- 10.1101/2023.08.27.554986 is OK
- 10.1016/j.chom.2023.05.025 is OK
- 10.1093/bioinformatics/bty419 is OK
- 10.1016/j.cell.2020.08.012 is OK
- 10.1126/science.abf9302 is OK
- 10.1093/ve/veac110 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 10 months ago

Wordcount for paper.md is 1804

editorialbot commented 10 months ago

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

csoneson commented 10 months ago

👋🏼 @WillHannon-MCB, @afrubin, @jkanche - this is the review thread for the submission. All of our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review checklist. 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!

WillHannon-MCB commented 10 months ago

Hi @csoneson! I'm looking forward to the review process. Is there anything specific that I need to do at present?

csoneson commented 10 months ago

Hi @WillHannon-MCB - no, nothing in particular at this point!

jkanche commented 9 months ago

Review checklist for @jkanche

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

csoneson commented 9 months ago

👋🏻 Hi all, happy new year! I just wanted to check in here after the holidays and make sure that everything is clear with the review process. @jkanche, @afrubin - let us know when you have some initial comments for the authors! Thanks all 🙂

jkanche commented 8 months ago

I'm planning on providing the technical review by next week. Hope that still works with the timeline.

csoneson commented 8 months ago

Sounds good - thanks @jkanche

csoneson commented 8 months ago

👋🏻 @afrubin - could you give an update on your review progress here? Thanks!

afrubin commented 8 months ago

@csoneson very sorry for the unexpected delay! I'll have my review completed this week.

csoneson commented 8 months ago

Thanks @afrubin!

afrubin commented 8 months ago

Review checklist for @afrubin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

afrubin commented 8 months ago

I'm looking forward to playing around with the tool some more and uploading some other DMS datasets, but I have some initial comments on the paper itself that I wanted to leave here since they aren't directly related to the software (and therefore less suited to becoming issues on that repo).

The introduction skips over a lot of basic information and launches right into some very specific applications from your lab. It seems like an extra sentence or two about the data and some key citations (like Fowler & Fields 2014 and some other more recent reviews) would be worth including. You might also want to cite the recent overview "An Atlas of Variant Effects to understand the genome at nucleotide resolution" to show the expected expansion of the field.

There are other visualization tools like ProtVar that could be mentioned.

The examples are currently all viral datasets, while most of the DMS data being generated is from human genes. This makes sense given the authors' research focus, but I recommend adding some more examples from diverse organisms generated by other labs to back up the claim that this is a general tool. There's a lot of data in MaveDB and I'll share my results as I try to visualize some of my favorite examples.

afrubin commented 8 months ago

I was able to successfully visualize my own dataset with the tool, and opened a number of issues on the repositories based on my experience. @WillHannon-MCB happy to answer any followup questions you might have here or in the above issue threads.

WillHannon-MCB commented 8 months ago

Thanks @afrubin! These are all great suggestions. I'll follow up with any questions I have as I start tackling each issue.

csoneson commented 7 months ago

👋🏻 Just wanted to check in here - I see there are a bunch of issues being worked on so it looks like things are moving, just let me know if there are any questions.

csoneson commented 7 months ago

👋🏻 @WillHannon-MCB, @afrubin, @jkanche - could you give a quick update of where things are standing here?

WillHannon-MCB commented 7 months ago

Sorry for the slow reply! I was a little sidetracked with another project. I'm currently working on the suggestions from @afrubin and @jkanche. Thank you for your patience!

afrubin commented 7 months ago

@csoneson I'm just waiting for the open issues to get addressed, after which I'd imagine things will move quickly toward acceptance.

Kevin-Mattheus-Moerman commented 6 months ago

@WillHannon-MCB I hope you are getting on well. Do you have any updates on the above? It would be great to proceed soon, to avoid loosing track of the reviewers.

WillHannon-MCB commented 6 months ago

Sorry, I was on vacation. I'm almost done addressing the reviewers issues. There are a few minor issues related to documentation that I'm currently working on.

WillHannon-MCB commented 6 months ago

@Kevin-Mattheus-Moerman, I think I've addressed all of the reviewer's comments. How do we proceed?

csoneson commented 6 months ago

Thanks @WillHannon-MCB - the next steps would be for @afrubin and @jkanche to take another look and see whether their comments were addressed (and if so, tick off the appropriate boxes in their checklists) and if there are additional comments.

csoneson commented 5 months ago

👋🏻 @afrubin, @jkanche - just wanted to check in here. Let us know when you have had a chance to look at the updated submission! Thanks a lot.

csoneson commented 5 months ago

Ping @afrubin, @jkanche - could you let us know when you think you will hvae a chance to look at the revised submission? Thanks!

👋🏻 @afrubin, @jkanche - just wanted to check in here. Let us know when you have had a chance to look at the updated submission! Thanks a lot.

afrubin commented 5 months ago

@csoneson Sorry for the lack of reply, I've been traveling. I should have this taken care of next week.

jkanche commented 5 months ago

me as well, hope to do this by next week

afrubin commented 5 months ago

@WillHannon-MCB the changes to the code all look great, thanks. However it doesn't look like the paper has been updated in response to my previous comments in the thread.

I also added one new issue (https://github.com/dms-viz/dms-viz.github.io/issues/85) that came up with a dataset I tried to visualize. That issue includes a copy of the .json file dms-viz is expecting with the scores, so you should feel free to add that to the examples if you want a non-viral one.

WillHannon-MCB commented 5 months ago

Thanks, @afrubin,. I'll address the new issue and post the updated paper tomorrow!

WillHannon-MCB commented 5 months ago

Hi @afrubin, I've updated the manuscript with your comments. The only thing missing is the link to a human example. I'm planning to use the PTEN VAMPseq dataset you sent. I've got a minimal example, but the scale limits are currently arbitrary. Would you mind sharing a configure-dms-viz command to make a meaningful visualization with this dataset?

I've also made it possible to set the center of the heatmap's scale. The updated documentation has the implementation details.

csoneson commented 4 months ago

👋🏻 Checking in here - @jkanche, did you have a chance to take a look at the updated submission? @afrubin - could you also give an update on where things are at from your perspective (it looks like the issues that were opened above have been closed, but most items in your checklist are unticked, so I just want to make sure I understand where we're standing 🙂)? Thanks!

jkanche commented 4 months ago

Thank you @afrubin for updating the paper, I t looks really good, a few comments.

Statement of need section, point (7). I would rephrase "local upload", makes me thing I'm uploading the file to the server hosting the application. It might help to explicitly state that the file loaded into the app is not uploaded into any servers since dms-viz is a pure front end visualization tool.

Design and usage section

Figure 3: I would make the labels more obvious: context, focus, ...

Let me know if you have any questions. Thank you for all the updates!

csoneson commented 4 months ago

Thanks @jkanche! I see you also have an unticked box for the automated tests in your checklist (in addition to the one regarding the paper). Is this still an outstanding issue?

jkanche commented 4 months ago

all good, @csoneson. probably my mistake as i was checking them off.

WillHannon-MCB commented 4 months ago

@jkanche, I updated the paper with your recommendations.

jkanche commented 4 months ago

Thank you for updating the paper, looks great!

csoneson commented 4 months ago

Hi @afrubin - could you give us a quick update on the status of your review here? Thanks!

@afrubin - could you also give an update on where things are at from your perspective (it looks like the issues that were opened above have been closed, but most items in your checklist are unticked, so I just want to make sure I understand where we're standing 🙂)? Thanks!

afrubin commented 4 months ago

@WillHannon-MCB Looks great, sorry for the delay in getting back to this! One very minor thing is that the link in the paper for the PTEN dataset doesn't seem to work. Here is an updated file that uses the --heatmap-limits option to set the midpoint of the heatmap to 0. It would obviously be better if the colors in the heatmap matched the protein colors, but I don't want to delay things further. pten_example.json

@csoneson Aside from the above, I think this is ready to progress to the next steps. Thank you for your kind reminders and your patience with my busy travel schedule!

csoneson commented 4 months ago

Thanks @afrubin!

WillHannon-MCB commented 4 months ago

@csoneson, I've updated the paper with @afrubin's data. Is there anything else that needs to be done?

csoneson commented 4 months ago

@editorialbot generate pdf

csoneson commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/ve/vead055 is OK
- 10.1101/2020.10.29.339317 is OK
- 10.1016/j.cell.2023.02.001 is OK
- 10.1186/s13059-019-1845-6 is OK
- 10.1186/s13059-023-02986-x is OK
- 10.1038/nmeth.3027 is OK
- 10.21105/joss.02353 is OK
- 10.1101/2023.08.27.554986 is OK
- 10.1038/s41588-018-0122-z is OK
- 10.1016/j.chom.2023.05.025 is OK
- 10.1093/bioinformatics/bty419 is OK
- 10.1016/j.cell.2020.08.012 is OK
- 10.1126/science.abf9302 is OK
- 10.1093/ve/veac110 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 4 months ago

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

csoneson commented 4 months ago

Thanks @WillHannon-MCB. Based on the checklists and the comments above, it looks like the reviewers are satisfied with the current state - @jkanche, @afrubin, could you confirm (for the record, and to make sure I did not overlook anything) whether this is the case?

In the meanwhile I will also take a look through the submission, and I'll get back to you shortly with the next steps.

afrubin commented 4 months ago

@csoneson looks good to me!