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[REVIEW]: Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer #1407

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whedon opened this issue Apr 23, 2019 · 99 comments

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commented Apr 23, 2019

Submitting author: @IbrahimTanyalcin (Ibrahim Tanyalcin)
Repository: https://github.com/IbrahimTanyalcin/lexicon-mono-seq
Version: v0.19.0
Editor: @csoneson
Reviewer: @hrhotz, @jkanche, @imallona
Archive: 10.5281/zenodo.3273310

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/9fbf126b501ad921825f755732450278"><img src="http://joss.theoj.org/papers/9fbf126b501ad921825f755732450278/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/9fbf126b501ad921825f755732450278/status.svg)](http://joss.theoj.org/papers/9fbf126b501ad921825f755732450278)

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

@hrhotz & @jkanche & @imallona, 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 @csoneson know.

Please try and complete your review in the next two weeks

Review checklist for @hrhotz

Conflict of interest

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?
  • Version: v0.19.0
  • Authorship: Has the submitting author (@IbrahimTanyalcin) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jkanche

Conflict of interest

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?
  • Version: v0.19.0
  • Authorship: Has the submitting author (@IbrahimTanyalcin) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @imallona

Conflict of interest

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?
  • Version: v0.19.0
  • Authorship: Has the submitting author (@IbrahimTanyalcin) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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commented Apr 23, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hrhotz, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

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:

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commented Apr 23, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Apr 23, 2019

PDF failed to compile for issue #1407 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1407 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

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commented Apr 23, 2019

@whedon generate pdf

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commented Apr 23, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Apr 23, 2019

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commented Apr 23, 2019

@labarba (or @openjournals/joss-eics) - just to say that the manual change of the path to the submitted repository in the PRE-REVIEW issue (#1379) did not seem to carry over here. I manually changed it again above, which I think should be fine for the review, but I'm not sure whether anything else needs to be changed somewhere for a more permanent effect.

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commented Apr 23, 2019

@hrhotz, @jkanche, @imallona - please perform your review in this issue, by updating your checklist above and posting comments. If you have any questions, don't hesitate to ping me.

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commented Apr 24, 2019

@IbrahimTanyalcin - I have made a pull request with some minor suggestions for the paper text.
Also, please consider adding the names of a few examples for browsers using DOM Text + SVG. Same for MSA viewers relying on the canvas element. This might help putting the text in a wider context.

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commented Apr 24, 2019

@hrhotz, ty for the suggestions:

  • merged your pull request
  • added names to the examples
  • added jsdelivr/npm link for downloading the script
  • added a minified version from jsdelivr (~40kB)
  • added 4 new citations, 2 tools that are similar (DOM text) to lexicon-mono-seq, and 2 that are canvas based (IGV and MSA Viewer)
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commented Apr 26, 2019

@IbrahimTanyalcin - I created a pull request with a few minor edits and fixes to the paper. Couple of things

  • version number of the release does not match the one in the paper
  • I'd consider adding this to examples
  • rename files in examples with specific names so that its easier to browse
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commented Apr 26, 2019

@jkanche, ty for the suggestions

  • merged your PR
  • add a new reference for ascii genome
  • changed the example names in the repo
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commented Apr 29, 2019

@IbrahimTanyalcin - I have been looking at the "clustalW.html" example and I have a few questions/comments:

    • what is the "aa" color scheme based on?
    • would it make sense to offer more than just one color set for amino acids?
    • how do you deal with sequences containing Selenocysteine? I have modified your example by replacing an "A" with and "U" and the complete sequence is no longer displayed,
    • why is the line describing the identity/similarity (the line containing "*",":", etc) not displayed
    • I don't understand your comment: "You can also read clustal files if you provide them to LexiconMonoSeq as a string". You already provide the data as a string in the example, don't-you?
    • displaying an alignment where you provide a file path would be useful.
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commented Apr 29, 2019

Hi @IbrahimTanyalcin,

Thanks for the resource. I have some comments/questions regarding the rendered PDF version of the paper, and the resource and its documentation.

I noticed the paper update has fixed some typos already (dna -> DNA), but I still find some in citations. Namely,

  • ES6 citation is currently is listed as (International, 2018) instead of (Ecma International, 2018).
  • The reference for lexicon library by Tanyalcin et al. does not indicate the journal name.
  • Also, this paper footpage Tanyalcin, (2019). doesn't list the author's full name, but only the last name.

Regarding the tool usability, it is stated that (...) the amount of sequences is limited to your browsers capacity, recommended limit is 8000 sequences with 100000 characters long each (...). Is it possible to tabulate/stratify such recommendation, i.e. providing a limit for commodity laptops as well as to recent/powerful machines/workstations?

Regarding the tool usability and/or documentation, I acknowledge the high flexibility given to the durations of animation effects, which (if I'm not wrong) can be quite short, i.e. 17ms. As intermittent visual stimuli are known to elicit epileptic seizures to some, I wonder which are your thoughts on including a warning at the resource documentation suggesting good practices. The W3C indicates that, in order to avoid triggering seizures to photosensitive epilepsy users, blinks should be slower than three a second https://www.w3.org/TR/2008/REC-WCAG20-20081211/#seizure . Not sure of the examples' animation speeds (the ones rendered at readme.md), but if they were faster than that I would suggest slowing them down to the W3C recommendations.

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commented Apr 30, 2019

@hrhotz Thank you for the well raised comments, let me go over some of these:

instance.registerType("myType",{"A":"#ffbbaa","B":"00aacc"...})

You can also specify a text color and opacity which are optional, default text color is rgb(0,0,0,0.9) and default opacity for any character is 0.8

Normally you do not have to create a new object from scratch to pass to instance.registerType as an argument, a copy function exists instance.caveManCopy on the prototype chain. Example-7(chrX10Mb.html in the repo examples folder) makes use of this. It registers a new type with new characters.

The error you encountered (things not rendering) is possibly because the new char you specified was not registered in the type and it threw Uncaught Reference Error, I am not using try/catch blocks there because I presume it would slow down execution.

  • For the similarity line with "*" character for Clustal.wl files, I initially thought the coloring would be sufficient to draw human perception to similar regions, but now after your comment I realize it might not be adequate. The static function that reads the clustal.wl is here and specifically this is the line that "discards" the lines with "*". I propose that we pass an optional argument to not filter out those lines. What do you think.

  • That is correct, I will revise that sentence, "also" is unnecessary. Thank you for pointing out.

  • Indeed, currently in the examples I use XMLHttp (not fetch for older browsers). I propose I add a static "fetch" function to read out clustal.wl files. An options arguments in the form of an object could be passed where keys:

    • retry : specify retry count upon failure
    • medium: either "local" (for file API) or "remote" (default, uses XMLHttp)
      The above would return a thenable object which you can chain later on. Is that ok?
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commented Apr 30, 2019

@imallona Thank you for pointing out these blind spots. I will go over the citations, did not realize that they were incomplete.

For the performance, I just tested the first example and the letters of PI on an old iphone 5S to see if it did render. The animations were not butter smooth, however it handled without problems (iphone 8 and X rendered without problems and with 60fps). Since we are working with DOM, we are mainly using CPU (apart from transform css style, which creates a layer for GPU) and this could be quite variable. That being said, since sequence length is not the bottle neck and to be on the safe side, we could say for most commodity laptops 1000 sequences with 100000 letters each could run reasonably smooth (since they run on iphone 5S). I have access to variety of different devices including android, iOS and Mac. If you have specific hardware let me know so I can test it on them.

About the epileptic seizures, thank you for raising this point! I must say I am completely ignorant in this field and I think it is a good idea to at least include some sort of disclaimer. For the duration, you are correct that the lowest you can go is 17ms (this is hardcoded in window.requestAnimationFrame API). The default duration is 1500milliseconds, this controls the sliding of the text. The colored boxes are filled with a default duration of 150ms with a limit of 80 characters per line. Another parameter is also the painter count (these are parallel async renderers), by default there is only 1 painter, an example where you can spawn more painters is here.

What above means is that, by default if a display has 15 sequences with a screen with of 120 characters, it would take Math.ceil(120/80) * 15 * 150 + (15-1) * 17 ~= 4750ms to fill the screen and the screen would briefly "update" 30 times within this period, that is roughly 6 "updates" per second which is twice the recommended range in the link you kindly provided.

I suggest we add a disclaimer, and for some examples like this, we could increase the duration to 350ms. What do you think?

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commented Apr 30, 2019

@IbrahimTanyalcin - Thanks for your feedback, please allow me to go a little bit deeper into some of my comments (which I now have numbered) wrt to the "clustalW.html" example:

    • your chosen "aa" color scheme does make sense. Though, you should probably acknowledge the person who set it up originally.
    • the option to add a custom color scheme is great. It might help if you document this (with a code example) in addition to the code example shown for the "asciiArt" and/or add the text you have written for "Example-7(chrX10Mb.html)" in this thread to the documentation. However, my actual comment was: whether it would make sense to have several pre-defined color schemes which you can chose from. As an example have a look at Jalview (http://www.jalview.org/)
    • an optional argument sound very good
    • sure, whatever is the easiest way to implement it, is fine
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commented May 2, 2019

Hi @IbrahimTanyalcin,

Thank you for your feedback. I see, so setting thresholds for performance is a difficult task due to the huge variety of hardware available. My comment arose from the paper's sentence The amount of sequences is limited to your browsers capacity, recommended limit is 8000 sequences with 100000 characters long each, which I found not very useful as it does not specify what hardware that recommendation applies to (as you say, CPU, operating system/browser). I think that, if updated to add the recommendations for commodity laptops/phones you kindly posted here (1000 sequences with 100000 letters each), that sentence would be more informative, what do you think?

As for the update rate I appreciate your reflection and agree with your suggestions of adding a disclaimer and slowing down some examples.

Aside, as a minor comment unrelated to the former, I just noticed the paper.md refers to version 0.17.3 (...)the library is about 42kB (as of version 0.17.3)(...); you might want to update both library version and its size. Also noticed that dna and ascii should be capitalized.

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commented May 8, 2019

👋 @hrhotz, @imallona, @jkanche, @IbrahimTanyalcin - just wanted to check in to see how things are going here! I can see that there are some unticked boxes in all the reviews, as well as some comments for @IbrahimTanyalcin. It would be great to have a quick status update - and please don't hesitate to let me know if there is anything I can do to facilitate.

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commented May 8, 2019

@csoneson @hrhotz @imallona ,
The reviews were great! They just covered a lot of blind spots that I never thought of. I had to pause for a week, because I am actually integrating this library into mutaframe.com:

example

Not in production yet, but almost there.
I'm getting back to the comments at the end of this week.
Hope that is ok.

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commented May 15, 2019

👋 @jkanche - just checking in on your review status. There are several unticked boxes in your checklist - could you provide some comments for @IbrahimTanyalcin explaining your current reservations in some more detail?

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commented May 18, 2019

@csoneson, I did send a pull request with suggestions and updates to the paper, and I was waiting to hear back from @IbrahimTanyalcin until he's ready for the review again since he said he's working on new updates and integration in his last comment

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commented May 18, 2019

Thanks for the update @jkanche. @IbrahimTanyalcin - do you have an estimate of when the reviewers could have an updated version to look at (you mentioned above that you would get back to the comments at the end of last week)?

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commented May 18, 2019

@csoneson, getting back to it this weekend :) I merged that pull request I think.

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commented Jul 8, 2019

Attempting to check references...
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commented Jul 8, 2019


OK DOIs

- 10.1109/MCSE.2018.011111125 is OK
- 10.1155/2018/1718046 is OK
- 10.1093/bioinformatics/btm404 is OK
- 10.1186/1756-0500-7-468 is OK
- 10.1093/bioinformatics/btw474 is OK
- 10.1038/nbt.1754 is OK
- 10.1093/nar/gkx273 is OK
- 10.1093/bioinformatics/btx007 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 8, 2019

@whedon generate pdf

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commented Jul 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 8, 2019

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commented Jul 8, 2019

@IbrahimTanyalcin - great! I think this looks good. To finalize, could you create a Zenodo archive and post the resulting DOI here? Please make sure that the authors and title are exactly the same for the Zenodo archive and the manuscript, and that the version is consistent everywhere.

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commented Jul 8, 2019

@csoneson , before I even submitted for JOSS, I went ahead and created one:
https://zenodo.org/record/3272107#.XSOFeOszapo

I just released a new release now (ARIES), so the badge does not work yet, I guess it will work in a couple of hours. But it seems like it has tracked all the versions correctly. Is that ok?

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commented Jul 8, 2019

Yes, the DOI of the latest release should be fine. However, the title and author list of the Zenodo archive must be the same as in your paper.

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commented Jul 8, 2019

@csoneson ok, I added .zenodo.json, hopefully the webhook will work and it'll be picked up.

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commented Jul 9, 2019

@IbrahimTanyalcin Just checked, and the Zenodo record still looks the same to me.

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commented Jul 9, 2019

👋 @csoneson the webhooks for zenodo works in a weird unpredictable way. I waited about half a day for things to be refreshed however I realized that won't happen.
So I went ahead and registered a new DOI manually. Is it better now?

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commented Jul 9, 2019

Ok, great. Yes, 10.5281/zenodo.3273310 looks fine.

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commented Jul 9, 2019

@whedon set 10.5281/zenodo.3273310 as archive

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commented Jul 9, 2019

OK. 10.5281/zenodo.3273310 is the archive.

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commented Jul 9, 2019

@whedon set v0.19.0 as version

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commented Jul 9, 2019

OK. v0.19.0 is the version.

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commented Jul 9, 2019

Ok @IbrahimTanyalcin - I'll send this off to the editor-in-chief on duty for the formal acceptance!

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commented Jul 9, 2019

@openjournals/joss-eics - we're ready to accept this paper!

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commented Jul 10, 2019

@whedon accept

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commented Jul 10, 2019

Attempting dry run of processing paper acceptance...
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commented Jul 10, 2019


OK DOIs

- 10.1109/MCSE.2018.011111125 is OK
- 10.1155/2018/1718046 is OK
- 10.1093/bioinformatics/btm404 is OK
- 10.1186/1756-0500-7-468 is OK
- 10.1093/bioinformatics/btw474 is OK
- 10.1038/nbt.1754 is OK
- 10.1093/nar/gkx273 is OK
- 10.1093/bioinformatics/btx007 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 10, 2019

Check final proof 👉 openjournals/joss-papers#828

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#828, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Jul 10, 2019

@whedon accept deposit=true

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commented Jul 10, 2019

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

@whedon whedon added the accepted label Jul 10, 2019

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commented Jul 10, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Jul 10, 2019

🚨🚨🚨 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 👉 openjournals/joss-papers#829
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01407
  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...

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commented Jul 10, 2019

@hrhotz, @jkanche, @imallona - many thanks for your reviews and to @csoneson for editing this submission

@IbrahimTanyalcin - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Jul 10, 2019

@whedon

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commented Jul 10, 2019

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01407/status.svg)](https://doi.org/10.21105/joss.01407)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01407">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01407/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01407/status.svg
   :target: https://doi.org/10.21105/joss.01407

This is how it will look in your documentation:

DOI

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