[REVIEW]: An Introduction to Applied Bioinformatics: a free, open, and interactive text.

whedon commented 6 years ago

Submitting author: @gregcaporaso (James Gregory Caporaso) Repository: https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics Version: 0.1.3-dev Editor: @tracykteal Reviewer: @AstrobioMike Archive: 10.5281/zenodo.1442796

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@AstrobioMike, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://jose.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @tracykteal know.

Review checklist for @AstrobioMike

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: Does the release version given match the repository release (0.1.3-dev)?
[x] Authorship: Has the submitting author (@gregcaporaso) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

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 :tada:.

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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: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-e0f72c5e8125/lib/whedon/processor.rb:57:infind_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: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-e0f72c5e8125/bin/whedon:99:in<top (required)>' 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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tracykteal commented 6 years ago

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.

arfon commented 6 years ago

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

arfon commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

AstrobioMike commented 6 years ago

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

tracykteal commented 6 years ago

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.

gregcaporaso commented 6 years ago

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

tracykteal commented 5 years ago

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!

labarba commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

labarba commented 5 years ago

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

labarba commented 5 years ago

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

gregcaporaso commented 5 years ago

@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!

labarba commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

labarba commented 5 years ago

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.

gregcaporaso commented 5 years ago

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!

labarba commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

labarba commented 5 years ago

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

gregcaporaso commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

gregcaporaso commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

gregcaporaso commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

gregcaporaso commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

gregcaporaso commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

gregcaporaso commented 5 years ago

@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.

labarba commented 5 years ago

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.

labarba commented 5 years ago

@whedon set 10.5281/zenodo.1442796 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.1442796 is the archive.

gregcaporaso commented 5 years ago

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

That's fixed now, thanks!

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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labarba commented 5 years ago

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

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

labarba commented 5 years ago

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

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