[REVIEW]: An Introduction to Applied Bioinformatics: a free, open, and interactive text. about jose-reviews HOT 51 CLOSED

Overall comments
I've gone through some sections in great detail (listed below), and I've looked through the rest briefly so far. Everything I've seen is very nicely done and already really well polished. And the content is stellar. For those sections I have gone through in detail, I have no problems with anything and could only think of very few suggestions that might improve things or help with clarity (to which the pull requests are linked below). Though I consider nothing I've suggested as necessary for me to happily offer my support for publication. This is clearly a well put together resource that will help many aspiring and current bioinformaticians (I'm certainly enjoying learning from it). I'm happy to continue going through sections in detail and providing my minor edits/suggestions to the repository if they are helpful, but in my opinion publication shouldn't wait until I have "fine-toothed" everything – I've certainly seen nothing I would consider problematic in the sections I've glanced through but just haven't gone through in a detailed fashion yet, and to wait for me to do so kind of feels like just waiting for a proofreader. But again that's just my opinion. Here are the sections I've covered in detail so far and links to the pull requests.

Sections covered in detail and pull requests to very minor edits/suggestions
Fundamentals: Pairwise-sequence alignments
Fundamentals: Sequence homology searching

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

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Attempting PDF compilation. Reticulating splines etc...

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PDF failed to compile for issue #27 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:in collect!'
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-e0f72c5e8125/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
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:in dispatch'
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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

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It seems like something in the paper.md isn't allowing it to compile, but it's not clear what it is. I'll see if there's more information in error logs.

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It seems like something in the paper.md isn't allowing it to compile, but it's not clear what it is. I'll see if there's more information in error logs.

I think the issue is with the URL for the repository. This should be the root of the Git repository, i.e.:

https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics

not 

https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics/blob/master/paper.md

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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--> Check article proof 📄 <--

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Thanks @AstrobioMike! Given that the checklist items apply to the lessons as a whole, and you're seeing general consistency throughout, I don't think we need another reviewer for other sections. I'll just give those sections a read through as a final check.

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Hi @tracykteal, any updates on this? Thank you!

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Thank you so much for your submission and I'm sorry for the delay.

I've read through the Getting Started section. I've also gone through installation for the interactive version, and used the materials through the Binder link. Documentation about how to use the resources and even report issues is well documented and everything works. I like the link to the Issue tracker for reporting issues, already providing a mechanism for feedback and discussion that isn't 'send email'. These resources meet the model of being both open educational materials and taking an open source approach.

@labarba this should be officially accepted and published. Thanks!

@gregcaporaso can you create an archive (on Zenodo, figshare, or other) and post the archive DOI here. Then we link to that DOI for the publication.

Thanks so much for this paper!

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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@gregcaporaso : Can you add DOIs to the journal entries in the References list?

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Also, the book by Dunn has a website: http://practicalcomputing.org
And did you miss the co-author? (Steven H. D. Haddock)

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@labarba, I've added DOIs for all of the references that have DOIs, and I've added the website and co-author to the Practical Computing reference. Thanks for spotting those!

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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There's something wrong still with the DOI links. The reference to Searls 2014, for example, links to https://doi.org/https://doi.org/10.1371/journal.pcbi.1003662, which does not resolve. Similar problem with Wilson 2016, plus a overfull line. Pls try to fix.

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Ok, I think that change should fix it. I had full URLs for these DOIs (e.g., https://doi.org/10.12688/F1000RESEARCH.3-62.V2) where I should have just had the DOI itself (e.g., 10.12688/F1000RESEARCH.3-62.V2. Sorry about that!

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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I just downloaded the paper PDF, checked the links to the DOIs, and they're still broken.

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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PDF failed to compile for issue #27 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12 0 12 0 0 43 0 --:--:-- --:--:-- --:--:-- 43
Error reading bibliography ./paper.bib (line 54, column 16):
unexpected "."
expecting letter, digit, white space, "#", "," or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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@labarba, this should be good now - I reviewed the proof and I think I addressed the issues you pointed out. The DOI requested by @tracykteal is 10.5281/zenodo.1442796.

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Thanks. The author list on the Zenodo entry does not match the author list on the paper. Zenodo auto-generates the author list from the committers on the repo, so you may need to manually edit the entry.

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@whedon set 10.5281/zenodo.1442796 as archive

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OK. 10.5281/zenodo.1442796 is the archive.

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The author list on the Zenodo entry does not match the author list on the paper.

That's fixed now, thanks!

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

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@AstrobioMike — Thank you for your review!
@tracykteal — Thanks for handling this submission as editor!
🙏

@gregcaporaso — Your paper is now published in JOSS! 🎉

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https://twitter.com/LorenaABarba/status/1047189766964498432

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Thank you @AstrobioMike, @tracykteal, and @labarba - it was great working with all of you on this!

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