[PRE REVIEW]: Powering single-cell analyses in the browser with WebAssembly

[editorialbot]

Submitting author: !--author-handle-->@LTLA<!--end-author-handle-- (Aaron Lun) Repository: https://github.com/kanaverse/kana Branch with paper.md (empty if default branch): submission Version: 3.0.13 Editor: !--editor-->@AoifeHughes<!--end-editor-- Reviewers: @yongrenjie, @llewelld Managing EiC: Kevin M. Moerman

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1054.6 files/s, 298758.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      59           1637            982          19601
CSS                             16            177             58           1006
TeX                              2             69              0            616
Markdown                         5             74              0            222
JSON                             2              0              0            119
YAML                             1              5              3             30
HTML                             1              7             21             19
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            87           1969           1064          21614
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1504

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0654-x is OK
- 10.2307/2346830 is OK
- 10.1109/TIT.1982.1056489 is OK
- 10.1093/nar/gkv007 is OK
- 10.1080/01621459.1979.10481038 is OK
- 10.21105/joss.00861 is OK
- 10.12688/f1000research.9501.2 is OK
- 10.1093/bioinformatics/btw777 is OK
- 10.1371/journal.pcbi.1006135 is OK
- 10.1145/3140587.3062363 is OK
- 10.1038/nmeth.3615 is OK
- 10.1101/118992 is OK
- 10.1093/bioinformatics/btt100 is OK
- 10.1101/2021.04.05.438318 is OK
- 10.1038/nrg3833 is OK
- 10.1016/j.immuni.2019.03.009 is OK
- 10.1038/nbt.4091 is OK
- 10.1038/s41590-018-0276-y is OK

MISSING DOIs

- 10.1101/590562 may be a valid DOI for title: Orchestrating single-cell analysis with Bioconductor
- 10.1038/nmeth.3038 may be a valid DOI for title: Epiviz: interactive visual analytics for functional genomics data
- 10.1038/s41467-017-02001-5 may be a valid DOI for title: Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing
- 10.1101/350868 may be a valid DOI for title: Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis
- 10.1101/121889 may be a valid DOI for title: HiGlass: web-based visual exploration and analysis of genome interaction maps
- 10.3233/ida-2007-11402 may be a valid DOI for title: In search of deterministic methods for initializing K-means and Gaussian mixture clustering
- 10.1186/s13059-016-0947-7 may be a valid DOI for title: Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

INVALID DOIs

- 10.1137/04060593 is INVALID

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@LTLA thanks for this submission. I am the AEiC for this track and here to help process initial steps.

• [ ] Can you check those potentially missing/invalid DOIs ☝️ You can call @editorialbot check references to check them again, and also use @editorialbot generate pdf to update the paper.

• [ ] Can you clarify the purpose of this pre-print: https://doi.org/10.1101/2022.03.02.482701 ? Are you pursuing publishing/submitting this work anywhere else?

[LTLA]

Thanks @Kevin-Mattheus-Moerman.

DOIs are mostly fixed. The "Orchestrating single-cell analysis with Bioconductor" citation is a bit tricky as it refers to a book that accompanies the publication of the same name, and the suggested DOI refers to the latter. The book itself doesn't have a DOI unfortunately, though I can ask the BioC folks if they provisioned one.

As for the pre-print: no, this JOSS submission is the only one, in terms of a peer-reviewed submission. There's a bit of a backstory here but the sanitized version is that I post to biorXiv so that people can read it, not as a prelude to journal submission. It also helps that I can stuff more details in the biorXiv one, as I had to cut a lot to meet JOSS guidelines.

[LTLA]

@editorialbot generate pdf

[editorialbot]

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

[LTLA]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0654-x is OK
- 10.1137/04060593X is OK
- 10.2307/2346830 is OK
- 10.1109/TIT.1982.1056489 is OK
- 10.1093/nar/gkv007 is OK
- 10.1080/01621459.1979.10481038 is OK
- 10.21105/joss.00861 is OK
- 10.12688/f1000research.9501.2 is OK
- 10.1093/bioinformatics/btw777 is OK
- 10.1371/journal.pcbi.1006135 is OK
- 10.1145/3140587.3062363 is OK
- 10.1038/nmeth.3615 is OK
- 10.1101/118992 is OK
- 10.1093/bioinformatics/btt100 is OK
- 10.1101/2021.04.05.438318 is OK
- 10.1038/nmeth.3038 is OK
- 10.1038/nrg3833 is OK
- 10.1038/s41467-017-02001-5 is OK
- 10.1038/s41467-019-09182-1 is OK
- 10.1016/j.immuni.2019.03.009 is OK
- 10.1038/nbt.4091 is OK
- 10.1038/s41590-018-0276-y is OK
- 10.1186/s13059-018-1486-1 is OK
- 10.3233/ida-2007-11402 is OK
- 10.1186/s13059-016-0947-7 is OK

MISSING DOIs

- 10.1101/590562 may be a valid DOI for title: Orchestrating single-cell analysis with Bioconductor

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@LTLA that DOI suggested seems appropriate :point_up:

[Kevin-Mattheus-Moerman]

@editorialbot invite @AoifeHughes as editor

[editorialbot]

Invitation to edit this submission sent!

[LTLA]

@editorialbot check references

[LTLA]

@Kevin-Mattheus-Moerman I've just used the suggested DOI for now (which links to the manuscript), but it's not quite right. I'll update it with the proper DOI to the actual book if it ever becomes available.

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0654-x is OK
- 10.1038/s41592-019-0654-x is OK
- 10.1137/04060593X is OK
- 10.2307/2346830 is OK
- 10.1109/TIT.1982.1056489 is OK
- 10.1093/nar/gkv007 is OK
- 10.1080/01621459.1979.10481038 is OK
- 10.21105/joss.00861 is OK
- 10.12688/f1000research.9501.2 is OK
- 10.1093/bioinformatics/btw777 is OK
- 10.1371/journal.pcbi.1006135 is OK
- 10.1145/3140587.3062363 is OK
- 10.1038/nmeth.3615 is OK
- 10.1101/118992 is OK
- 10.1093/bioinformatics/btt100 is OK
- 10.1101/2021.04.05.438318 is OK
- 10.1038/nmeth.3038 is OK
- 10.1038/nrg3833 is OK
- 10.1038/s41467-017-02001-5 is OK
- 10.1038/s41467-019-09182-1 is OK
- 10.1016/j.immuni.2019.03.009 is OK
- 10.1038/nbt.4091 is OK
- 10.1038/s41590-018-0276-y is OK
- 10.1186/s13059-018-1486-1 is OK
- 10.3233/ida-2007-11402 is OK
- 10.1186/s13059-016-0947-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@LTLA oh right, sorry I might have been doing there. That DOI send to point to a preprint. Just ensure it is accurate, if it doesn't have a DOI, that is fine too.

[Kevin-Mattheus-Moerman]

@editorialbot invite @AoifeHughes as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@LTLA from the inspection report it looks like the core functionality of your work is encapsulated by 19601 lines of JavaScript. Can you please clarify the amount of Javascript that you wrote (rather than libraries you might have imported). Perhaps you can point to specific files that capture your contribution? Thanks.

[Kevin-Mattheus-Moerman]

@editorialbot invite @AoifeHughes as editor

[editorialbot]

Invitation to edit this submission sent!

[LTLA]

@Kevin-Mattheus-Moerman

I don't believe that the source repository contains any vendored libraries (other than a 400-line Pong game that we put in to distract users while the results were computing). @jkanche would know better, but AFAIK, most of that JS was handwritten for this app. For example, this file is already 1.4 kLoC, and the other files are probably around about the same size. I guess UI development is just verbose; better to have complex code than to have a complex user experience.

If it's any consolation, the code for the kana application is just the tip of the JS iceberg. Underneath kana, there is the bakana library that orchestrates the compute pipeline. And underneath that, there is scran.js, which performs the individual compute steps. And underneath that, there are a dozen C++ libraries that each probably warrant their own submissions.

[jkanche]

that is correct, except for the game files here, everything is handwritten.

app is based on npm, none of the libraries are vendored.

[Kevin-Mattheus-Moerman]

@editorialbot assign @AoifeHughes as editor

[editorialbot]

Assigned! @AoifeHughes is now the editor

[AoifeHughes]

Hello @LTLA, apologies for the delay in getting started. I'm just beginning my search for some reviewers. Do you have anyone in mind who would be appropriate to review? You can use: https://reviewers.joss.theoj.org/reviewers and I can reach out to them.

[LTLA]

Hi @AoifeHughes, I picked a few appropriate names from the list based on "Javascript + bioinformatics"

• Robaina
• kblin
• holtgrewe
• camillescott

Hopefully a few of them will be interested.

Would you like some suggestions for people outside this list?

[AoifeHughes]

This is great to start with thanks. I'll reach out now.

[AoifeHughes]

:wave: @robaina, @kblin, @holtgrewe, @camillescott, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[AoifeHughes]

@editorialbot add @yongrenjie as reviewer

[editorialbot]

@yongrenjie added to the reviewers list!

[AoifeHughes]

@editorialbot add @llewelld as reviewer

[editorialbot]

@llewelld added to the reviewers list!

[AoifeHughes]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5603.