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[REVIEW]: MiNAA: Microbiome Network Alignment Algorithm #5448

Closed editorialbot closed 8 months ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@crsl4<!--end-author-handle-- (Claudia Solis-Lemus) Repository: https://github.com/solislemuslab/minaa Branch with paper.md (empty if default branch): Version: V1.1.0 Editor: !--editor-->@graciellehigino<!--end-editor-- Reviewers: @Becheler, @salix-d Archive: 10.5281/zenodo.10625654

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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

@Becheler & @waynebhayes, 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 @graciellehigino 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 @Becheler

📝 Checklist for @salix-d

Kevin-Mattheus-Moerman commented 1 year ago

@salix-d folks can most certainly volunteer. Our documentation for reviewers lives here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you can confirm you have no conflict of interest I can consider assigning you as reviewer if you like.

salix-d commented 1 year ago

I can confirm I have no conflict of interest 🙂 I had done another JOSS review in May and was interested in this one too! I was sorry to see it didn't work out with the other reviewer 🙁

crsl4 commented 1 year ago

Thanks so much @salix-d

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot add @salix-d as reviewer

editorialbot commented 1 year ago

@salix-d added to the reviewers list!

graciellehigino commented 1 year ago

Yay, thank you @salix-d ! I'm happy to see you can contribute!

salix-d commented 1 year ago

Review checklist for @salix-d

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

salix-d commented 1 year ago

Hi! Got stucked at the 'Installation' point today; see https://github.com/solislemuslab/minaa/issues/6.

reednel commented 1 year ago

Hi @salix-d! I'm sorry you hit a snag on my instructions, but I appreciate your detailed explanation. I've just pushed an update to the readme.

salix-d commented 1 year ago

I also hit a bigger snag trying to make my c++ work on VScode but that was VScode issues ^^' (paths not being updated properly in the config json files type of thing)

Now that I got that working, I did hit another small bump 😅 The file_io.cpp script is a bit too specific on the slashes allowed in files' name: see https://github.com/solislemuslab/minaa/issues/7

On one hand, I'm a bit annoyed at Windows for always having more issues. On the other, I'm glad your software gets tested on it otherwise they wouldn't have been noticed. 😄

reednel commented 1 year ago

Ah, originally I did expect Windows users to always use backslashes, and it was an oversight to not specify the slightly different example command for their case. But I like the simplicity of your suggested code, so I'll verify its behavior and push an update this evening. My MiNAA development flip-flopped between Ubuntu and MacOS environments, but I only retroactively added support for Windows systems, so I confess my testing was much more limited there. I'm glad we can smooth out some bumps as well.

salix-d commented 1 year ago

In that case, you might want to know that Windows has no problem running .sh files, so you didn't really need to do the .bat one.

Re: the code

I did managed to run the examples and the simulations with no more problems 😄 I also tried the simulation with a different alpha value (0.6) to see if it would give similar results. heatmap_a06_web

Re: the documentation

In the README file, in the example section, the code doesn't use the names of the file in the example folder. I understand using more generic variable names as 'network0' and 'network1', but I would probably mention that there's a readme file and example data in the example folder, so if they want to try the examples they should use that code.

The 2nd example uses a 'bio_costs.csv' but there's no equivalent provided in the example folder, so we can't really test that functionality. Since being able to include measures of biological similarity seemed to be an important aspect of this tool, I would have expected an example of it. It's also not examplified in the paper.

Re: the paper

I found one spelling error on line 102 "for the same networs"; should be "networks". I noticed that the legend of figure 2 isn't labeled or described in the figure's text.

reednel commented 1 year ago

In the latest push

The point about our absense of an example using biological data warrants discussion with @crsl4.

I'm keeping simulations/align.bat around for now because on my own Windows machine, I am not able to run simulations/align.sh, and from what I can find online, Windows cannot run bash scripts in the ordinary command line.

Becheler commented 1 year ago

I also hit a bigger snag trying to make my c++ work on VScode but that was VScode issues ^^' (paths not being updated properly in the config json files type of thing)

Now that I got that working, I did hit another small bump 😅 The file_io.cpp script is a bit too specific on the slashes allowed in files' name: see solislemuslab/minaa#7

On one hand, I'm a bit annoyed at Windows for always having more issues. On the other, I'm glad your software gets tested on it otherwise they wouldn't have been noticed. 😄

Just a quick fact (not even a suggestion, it's beyond the scope of this article), but Visual Studio Code has a Devcontainer extension that allows you to connect to Docker (the Docker app just has to be open in the background) and quickly sets up whatever image you defined in your project .devcontainer/Dockerfile file and .devcontainer/devcontainer.json. Super easy to setup, so the user litterally just have to click on "open in container", and then click on whatever task you defined in your .vscode/tasks.json file (for example a "Compile and Run Tests" task). Very cool feature ;)

salix-d commented 1 year ago

I'm keeping simulations/align.bat around for now because on my own Windows machine, I am not able to run simulations/align.sh, and from what I can find online, Windows cannot run bash scripts in the ordinary command line.

I wasn't saying you should remove it, I though maybe it had just been extra work. Maybe it worked for me because I was using the mingw terminal and not the windows command prompt 🤔 Either way, better to have more option than less.

Also, yeah Windows is a bit weird sometimes. I could run everything from VS Code except the python part. I was able to run it from R Studio, in the terminal though 🤷‍♂️

reednel commented 1 year ago

The point about our absense of an example using biological data warrants discussion with @crsl4.

Following up on this: Claudia, Rosa, and I are working out a method to synthesize the biological component. The tentative idea is a new R script that constructs a phylognentic tree for the nodes in the networks, and produces a distance matrix from there. We'll keep you updated as we go.

graciellehigino commented 10 months ago

Hi all! Happy New Year! How is this progressing? Do you have any updates @reednel ?

reednel commented 10 months ago

Happy new year @graciellehigino! The end of semester and holidays have made progress slow on our end. Claudia, Rosa and I meet on Friday to discuss our plan, and if we come away with relevant updates I'll share those here. Apologies for the delay.

graciellehigino commented 10 months ago

No worries! Just checking in 😊 Let us know if you need anything!

reednel commented 10 months ago

We're going to get real data to construct a full example that includes the use of a meaningful biological matrix in the alignment. We can't say exactly when it will be ready, as we're depending on a couple others to get us the data and assemble it into something usable. But it's a priority for us so we can push this paper through. Once we get this example in and add it to the documentation, I believe we will have satisfied the remaining boxes on Salix's checklist :)

reednel commented 10 months ago

We've pushed a reproducible example that uses real biological data, and a couple others. All can be found in the examples folder. At the same time we've pulled in additional updates we've been developing. For the full list of changes, see my notes on the PR. To be clear, core functionality is the same, everything described in the manuscript is still accurate, and any previously run commands and inputs would yeild the same output. All new features are purely additional and optional. @salix-d and @Becheler, these features are documented in the README and examples of their usage are in the same examples folder if you'd like to look them over. Let me know of any questions or concerns. Thank you!

salix-d commented 10 months ago

Checklist completed 🚀

crsl4 commented 10 months ago

Fantastic news, thanks @salix-d !!

crsl4 commented 10 months ago

@graciellehigino what are the next steps?

graciellehigino commented 10 months ago

Amazing job, folks! Thank you so much for helping out @salix-d !

graciellehigino commented 10 months ago

@editorialbot generate pdf

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:

graciellehigino commented 10 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

graciellehigino commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/bibm49941.2020.9313552 is OK
- 10.18637/jss.v071.i10 is OK
- 10.1098/rsif.2010.0063 is OK
- 10.1186/1471-2105-12-24 is OK
- 10.1002/nav.20053 is OK
- 10.1016/j.csbj.2020.09.011 is OK
- 10.1093/bioinformatics/btv130 is OK
- 10.4137/cin.s680 is OK
- 10.1093/bioinformatics/btt202 is OK
- 10.1101/2020.07.15.195248 is OK
- 10.13140/RG.2.1.3572.3287 is OK
- 10.1093/bioinformatics/btq091 is OK
- 10.1186/s12864-019-5471-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
graciellehigino commented 10 months ago

@crsl4 and @reednel could you go through this checklist with me before I recommend it for publication?

reednel commented 10 months ago

Yes we'll get on that, thanks @graciellehigino. For box 2, the latest release with all changes from the review is 1.1.0.

reednel commented 10 months ago

@graciellehigino on Zenodo I have the option to set the DOI or create a new one. Should I generate one or use one from the bot's list above, or somehwere else? Edit: same thing with Figshare. Should these share a DOI?

reednel commented 9 months ago

Zenodo

Figshare

@graciellehigino All checkboxes on our side can be ticked. Let us know if anything needs revision.

crsl4 commented 9 months ago

Hi @graciellehigino , just checking if we can move forward with this paper. It seems all is done on our end. Thanks!

crsl4 commented 8 months ago

Hi @graciellehigino, sorry to keep bothering you! Any updates from you? We are just waiting on your editor last tasks. I tag @Kevin-Mattheus-Moerman in case he can help us more forward as well. Thanks!

graciellehigino commented 8 months ago

@editorialbot set 1.1.0 as version

editorialbot commented 8 months ago

Done! version is now 1.1.0

graciellehigino commented 8 months ago

@editorialbot set https://doi.org/10.5281/zenodo.10625654 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10625654

graciellehigino commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

graciellehigino commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/bibm49941.2020.9313552 is OK
- 10.18637/jss.v071.i10 is OK
- 10.1098/rsif.2010.0063 is OK
- 10.1186/1471-2105-12-24 is OK
- 10.1002/nav.20053 is OK
- 10.1016/j.csbj.2020.09.011 is OK
- 10.1093/bioinformatics/btv130 is OK
- 10.4137/cin.s680 is OK
- 10.1093/bioinformatics/btt202 is OK
- 10.1101/2020.07.15.195248 is OK
- 10.13140/RG.2.1.3572.3287 is OK
- 10.1093/bioinformatics/btq091 is OK
- 10.1186/s12864-019-5471-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 8 months ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

citation kurtz2015sparse not found
graciellehigino commented 8 months ago

Congratulations, everyone! 🎉

editorialbot commented 8 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid. 

IDREFS attribute rid references an unknown ID "ref-kurtz2015sparse"
graciellehigino commented 8 months ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

citation kurtz2015sparse not found

@crsl4 @reednel oops, I let it slide this reference! Could you fix it? As soon as you do, @Kevin-Mattheus-Moerman will be able to proceed with acceptance [=

reednel commented 8 months ago

@graciellehigino @Kevin-Mattheus-Moerman the reference has been added to paper/paper.bib!