Joss-reviews: [PRE REVIEW]: mzEasy

[whedon]

Submitting author: @chasemc (Chase M Clark)
Repository: https://github.com/chasemc/mzEasy
Version: 0.1.0
Editor: @arfon
Reviewers: @biswapriyamisra, @mwang87

Author instructions

Thanks for submitting your paper to JOSS @chasemc. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@chasemc if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #804 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

[chasemc]

I did some searching but am currently unsure the reason the PDF isn't compiling.

@biswapriyamisra may be suited for this review

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[biswapriyamisra]

I am willing to do a peer-review as an invited reviewer.

Thanks,
Biswa

[biswapriyamisra]

1. Fairly quick and easy installation when MSConvert and R 3.5 or so are in place!
2. Useful too for the conversions.
3. More comments and suggestions in the annotated PDF.
4. Useful tutorial and walk through images.

mzEasy_JOSS_Reviewer_Comments.pdf

Thanks for the opportunity to review and all the best. Shall keep adding requests to more functionalities or issues when faced.

Thanks,
Biswa

[arfon]

@bovee - would you be willing to review this submission for JOSS?

[arfon]

Thanks for the opportunity to review and all the best. Shall keep adding requests to more functionalities or issues when faced.

Thanks so much for working on this already @biswapriyamisra. We've not yet assigned an editor to this submission and so the formal review hasn't actually started. Once we've found a second reviewer, I can go ahead and set up the review thread. This should be super-quick for you given the time you've already spent reviewing here :-)

[arfon]

@whedon assign @arfon as editor

[whedon]

OK, the editor is @arfon

[bovee]

Sorry, I'm currently on vacation without a computer (it'd be at least a
week before I'm able to) and I don't have access to a Windows box (skimming
over, it looks like installation requires Windows). If it can be used on
Mac/Linux and the delay's not a problem, I'd be happy to review though.

On Jul 7, 2018 1:24 PM, "Arfon Smith" [e-mail] wrote:

@bovee https://github.com/bovee - would you be willing to review this
submission for JOSS?

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You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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[arfon]

OK thanks @bovee.

If it can be used on Mac/Linux and the delay's not a problem, I'd be happy to review though.

@chasemc - can this software be used on Mac/Linux?

[chasemc]

Unfortunately not, I was waiting to address this as it was also a comment here (https://github.com/openjournals/joss-reviews/issues/804#issuecomment-403182850).

The reliance on MSConvert to convert spectra is necessary, and MSConvert itself relies on vendor dll files that require a Windows operating system. There are workarounds for Linux and Mac, but they remain buggy and incomplete (https://sourceforge.net/p/proteowizard/mailman/message/35780564).

[arfon]

@chasemc - could you take a look at this list of viewers and see if you can identify any other potential candidates? https://bit.ly/joss-reviewers

[arfon]

Also, feel free to nominate anyone you are aware of professionally that might be able to review that isn't in this list.

[chasemc]

@mwang87 would you still be able to review? I know you said Windows machines are hard to come by.

[chasemc]

If not- maybe @lgatto could or would know someone.

[mwang87]

@chasemc Would be happy to review. I have my personal windows machine at home that I can install it on.

--Ming

[lgatto]

@chasemc - I don't have any windows computer at hand for the moment, and won't before a couple of months.
What about @jotsetung? Or @vladpetyuk? Do you have access to a windows.

[chasemc]

@arfon How many reviewers does JOSS usually have? I can see if I can suggest others if needed.

[arfon]

@chasemc - ideally two or more.

[jorainer]

I do have a Windows (7) virtual machine for testing purposes, but I'm still in post-vacation stress and quite busy the next weeks.

[chasemc]

I think mass spec is especially well covered. I went through the google doc again and think the following people (in no specific order) would also be qualified for review.
@juanvillada
@road2stat
@skummerf
@mschubert
@semacu

[arfon]

:wave: @jotsetung - would you be able to commit to reviewing this package by mid-September?

[jorainer]

sorry @arfon but I'm still too busy - unexpected stuff going on here, sorry again

[arfon]

@juanvillada, @road2stat, @skummerf, @mschubert, @semacu - 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

[mschubert]

I don't have a Windows box. - Judging from the comments, this seems to be a requirement.

[nanxstats]

Thanks for the invitation @arfon , but I don't have access to Windows machines either... 😂

[semacu]

I am unable to grade the submission as I am not an expert on this area and I do not have access to a Windows machine to try / test mzEasy in detail. Here are some points though:

• It would be useful if the paper could mention any ongoing research projects ot recent publications using mzEasy specifically
• Contains MIT LICENSE file
• Statement of need: it would be useful if the author could spell out both in the paper and the documentation the meaning of the acronym GNPS
• Installation instructions: Good, some dependencies (RInno / DesktopDeplyR) seem to be automatically installed after running the exe installer. However others (Proteowizard) require separate installation. Can all the different dependencies be installed at once?
• No example usage presented in the README. Please include a step-by-step example of how to use mzEasy in a real dataset.
• Contains guidelines in CONTRIBUTING.md
• I could not try / test mzEasy as I don't have access to Windows (In a separate note, it'd be good to include an extra column in the joss_reviewers excel sheet to add a list of accessible OS by each potential reviewer)

[chasemc]

Thank you for your time @semacu. I've informally outlined some responses below.

• It would be useful if the paper could mention any ongoing research projects ot recent publications using mzEasy specifically
  
  
  
  • I don't personally have any current projects using it, but certainly will within the next 6 months and it would have been useful for past work. It has been downloaded > 70 times in 10 countries and I personally know a few people using it, but no publication.
  
  
• Statement of need: it would be useful if the author could spell out both in the paper and the documentation the meaning of the acronym GNPS
  
  
  
  • Will do!
  
  
• Installation instructions: Good, some dependencies (RInno / DesktopDeplyR) seem to be automatically installed after running the exe installer. However others (Proteowizard) require separate installation. Can all the different dependencies be installed at once?
  
  
  
  • Unfortunately not for Proteowizard for the same reason the program requires Windows (https://github.com/openjournals/joss-reviews/issues/804#issuecomment-403336901)- the vendor-supplied dlls in Proteowizard are windows based and the vendor-licenses are not all open for secondary distribution.
  
  
• No example usage presented in the README. Please include a step-by-step example of how to use mzEasy in a real dataset.
  
  
  
  • Will do!
  
  

Thanks again for the extra effort.
-Chase

[juanvillada]

Thanks for the invitation @arfon. I am sorry, I could have access to a Windows machine on the weekend, but I am not experienced enough to judge a submission in this area.

[arfon]

@whedon add @biswapriyamisra as reviewer

[whedon]

OK, @biswapriyamisra is now a reviewer

[arfon]

@whedon add @mwang87 as reviewer

[whedon]

OK, @mwang87 is now a reviewer

[arfon]

Reading back up this thread, I'd forgotten that @biswapriyamisra had kindly carried out a pre-review of this submission already. I'm hoping he's willing to help us with the main review too 😄

[arfon]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/928. Feel free to close this issue now!

[arfon]

@biswapriyamisra, @mwang87 - I've gone ahead and set up the main review issue over in #928. Any questions/comments/feedback should be in that issue please.