[REVIEW]: starfish: scalable pipelines for image-based transcriptomics

[whedon]

Submitting author: @neuromusic (Justin Kiggins)
Repository: https://github.com/spacetx/starfish
Version: 0.2.2
Editor: @csoneson
Reviewer: @giovp, @shazanfar, @vals
Archive: 10.5281/zenodo.4734993

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Markdown: [![status](https://joss.theoj.org/papers/e00429a8b9030f0a231c870f9602ea7d/status.svg)](https://joss.theoj.org/papers/e00429a8b9030f0a231c870f9602ea7d)

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

Review checklist for @giovp

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 (@neuromusic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

Review checklist for @shazanfar

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 (@neuromusic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

Review checklist for @vals

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 (@neuromusic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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. @giovp, @shazanfar, @vals 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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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.1016/j.cell.2019.05.031 is OK
- 10.1016/j.cell.2018.05.035 is OK
- 10.1038/nmeth.3252 is OK
- 10.1186/s13059-017-1382-0 is OK
- 10.1073/pnas.1612826113 is OK
- 10.1038/nmeth.2563 is OK
- 10.1038/s41592-018-0175-z is OK
- 10.1093/nar/gkx1206 is OK
- 10.1126/science.aat5691 is OK
- 10.5281/zenodo.59499 is OK
- 10.7717/peerj.453 is OK
- 10.5281/zenodo.3710410 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[csoneson]

👋 @giovp, @shazanfar, @vals - thanks for accepting to review this submission! This is where the review will take place. In the post above you can find your respective checklists, and some additional information and instructions. Don't hesitate to ping me if you have any questions!

[csoneson]

@whedon re-invite @vals as reviewer

[whedon]

OK, the reviewer has been re-invited.

@vals please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[giovp]

To me, first round of review finished, would like to see spacetx/starfish#1899 addressed, in order to explore results.

[vals]

First round finished from my end as well. I would like all my issues addressed. But most importantly from my end there should be versions of the practical examples that can be read without running the notebooks ( spacetx/starfish#1904 ). Even when napari is used, the authors could make versions with screenshots. There is a lot of documentation about all the functionality, but without examples it is hard to get an understanding what the different functionality does.

[csoneson]

Thanks @giovp and @vals for your reviews! @shazanfar - could you give a quick update on the status on your side? Thanks!

[shazanfar]

Thanks for your patience @csoneson ! I've now completed the first round. I agree with @giovp and @vals comments regarding example data and including output in the tutorials. I've also requested amendments & clarification to do with scope + target audience, which I think would make the documentation more easily accessible for users. Thanks again! Cheers, Shila

[csoneson]

Thanks @shazanfar!
@neuromusic - looks like you got some good comments from the reviewers (and that you already started working on some of them 😃). Let me know if you have any questions, and when you are ready for the reviewers to take another look. Thanks!

[neuromusic]

Thanks all! @mattcai and I have started addressing a few of your comments and issues and we will follow up on the rest in the coming weeks.

[neuromusic]

Quick question: How would you prefer we handle closing issues when we feel like we've addressed them? Should we close them or is it best to wait for our reviewers to close them when they are happy?

[neuromusic]

ok, finally cut the release & updated zenodo info.

there was no additional development besides fixing some dependencies for the release.

DOI here: 10.5281/zenodo.4734993

[neuromusic]

& zenodo link here: https://zenodo.org/record/4734993

[csoneson]

@whedon generate pdf

[whedon]

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

[csoneson]

@whedon check references

[whedon]

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

OK DOIs

- 10.1016/j.cell.2019.05.031 is OK
- 10.1016/j.cell.2018.05.035 is OK
- 10.1038/nmeth.3252 is OK
- 10.1186/s13059-017-1382-0 is OK
- 10.1073/pnas.1612826113 is OK
- 10.1038/nmeth.2563 is OK
- 10.1038/s41592-018-0175-z is OK
- 10.1093/nar/gkx1206 is OK
- 10.1126/science.aat5691 is OK
- 10.5281/zenodo.59499 is OK
- 10.7717/peerj.453 is OK
- 10.5281/zenodo.3710410 is OK
- 10.1371/journal.pone.0228760 is OK
- 10.1093/nar/gkaa312 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[csoneson]

@whedon set 10.5281/zenodo.4734993 as archive

[whedon]

OK. 10.5281/zenodo.4734993 is the archive.

[csoneson]

@whedon set 0.2.2 as version

[whedon]

OK. 0.2.2 is the version.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[csoneson]

Thanks @neuromusic! I'm handing this over now to the AEiC on rotation for the last checks.

[whedon]

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

OK DOIs

- 10.1016/j.cell.2019.05.031 is OK
- 10.1016/j.cell.2018.05.035 is OK
- 10.1038/nmeth.3252 is OK
- 10.1186/s13059-017-1382-0 is OK
- 10.1073/pnas.1612826113 is OK
- 10.1038/nmeth.2563 is OK
- 10.1038/s41592-018-0175-z is OK
- 10.1093/nar/gkx1206 is OK
- 10.1126/science.aat5691 is OK
- 10.5281/zenodo.59499 is OK
- 10.7717/peerj.453 is OK
- 10.5281/zenodo.3710410 is OK
- 10.1371/journal.pone.0228760 is OK
- 10.1093/nar/gkaa312 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2276

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2276, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@csoneson You made this so easy! Thanks for sending this on so ready to go!! We can move this right on through the system since I see no errors or additional items to take care of.

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.02440 joss-papers#2277
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02440
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...

[kthyng]

Congrats on your new publication @neuromusic! Thanks to editor @csoneson and reviewers @giovp, @shazanfar, and @vals for your time, expertise, and hard work!

[whedon]

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

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