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Reference format #233

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agitter opened this issue May 31, 2019 · 5 comments · Fixed by #228
Closed

Reference format #233

agitter opened this issue May 31, 2019 · 5 comments · Fixed by #228
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plos Issues related to submission requirements for publication at PLOS Computational Biology

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@agitter
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agitter commented May 31, 2019

Your references need to be formatted according to the PLOS style. PLOS uses the numbered citation (citation-sequence) method and first six authors, et al. Authors should be listed as "Last name, First Initial". If using EndNote, please use the following style file: https://endnote.com/style_download/plos-public-library-of-science-all-journals/

See https://editor.citationstyles.org/styleInfo/?styleId=http%3A%2F%2Fwww.zotero.org%2Fstyles%2Fplos-computational-biology
@dhimmel
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dhimmel commented May 31, 2019

See #228

@dhimmel dhimmel mentioned this issue May 31, 2019
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@agitter agitter mentioned this issue May 31, 2019
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@dhimmel dhimmel added the plos Issues related to submission requirements for publication at PLOS Computational Biology label May 31, 2019
@dhimmel
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dhimmel commented Jun 11, 2019

More info at https://journals.plos.org/ploscompbiol/s/submission-guidelines#loc-references

@dhimmel dhimmel mentioned this issue Jun 11, 2019
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@agitter
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agitter commented Jun 11, 2019

One formatting question I'm still unclear about is whether they will take all of our inline links throughout the text. Do we need to reformat those as URL citations?

@dhimmel
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dhimmel commented Jun 13, 2019

Do we need to reformat those as URL citations?

I'm opposed to polluting our reference section with hyperlinks. Is there any indication that PLOS CB want us reformat hyperlinks as citations?

I would say we just wait to the proof stage to see if they make it though. I think their system is technically capable of publishing hyperlinks, although there is a chance they get removed by the default workflow.

@agitter
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agitter commented Jun 13, 2019

No, I haven't seen any indication that they want us to change the hyperlinks. I checked a few papers from their current home page and saw that they write out the URL for hyperlinks:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007044

  • OpenCV ver. 3.3.1 (https://opencv.org/).
  • ImageJ (https://imagej.nih.gov)

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007056

  • Los Alamos HIV Database (http://www.hiv.lanl.gov/)
  • PyMol (https://pymol.org/2/)

I'm okay leaving our links in their current format for the resubmission.

dhimmel added a commit that referenced this issue Jun 13, 2019
@dhimmel
Cleanup PLOS styled references
9b7427b 
Merges #241
Refs #233

* Add additional example manuscripts & citations

* Update frozen references

* Switch raw:dongbo-conversation to raw:paywall-movie. Now appears as:
21. Paywall: The Business of Scholarship [Internet]. 2018. Available:
https://paywallthemovie.com/paywall

Fixing of individual references as follows:

* Fix math in reference title for doi:10.1103/physrevlett.114.191803
use title from https://www.ncbi.nlm.nih.gov/pubmed/26024162

* Update Kipoi citation
Preprint has been published.

* Remove errant DOI for https://hdl.handle.net/10261/160086

* Update Silva et al from preprint to mSphere DOI

* Add book publisher place
agitter pushed a commit that referenced this issue Jun 13, 2019
@dhimmel
Cleanup PLOS styled references
2c69922 
This build is based on
9b7427b.

This commit was created by the following Travis CI build and job:
https://travis-ci.org/greenelab/meta-review/builds/545347524
https://travis-ci.org/greenelab/meta-review/jobs/545347526

[ci skip]

The full commit message that triggered this build is copied below:

Cleanup PLOS styled references

Merges #241
Refs #233

* Add additional example manuscripts & citations

* Update frozen references

* Switch raw:dongbo-conversation to raw:paywall-movie. Now appears as:
21. Paywall: The Business of Scholarship [Internet]. 2018. Available:
https://paywallthemovie.com/paywall

Fixing of individual references as follows:

* Fix math in reference title for doi:10.1103/physrevlett.114.191803
use title from https://www.ncbi.nlm.nih.gov/pubmed/26024162

* Update Kipoi citation
Preprint has been published.

* Remove errant DOI for https://hdl.handle.net/10261/160086

* Update Silva et al from preprint to mSphere DOI

* Add book publisher place
agitter pushed a commit that referenced this issue Jun 13, 2019
@dhimmel
Cleanup PLOS styled references
a7241ff 
This build is based on
9b7427b.

This commit was created by the following Travis CI build and job:
https://travis-ci.org/greenelab/meta-review/builds/545347524
https://travis-ci.org/greenelab/meta-review/jobs/545347526

[ci skip]

The full commit message that triggered this build is copied below:

Cleanup PLOS styled references

Merges #241
Refs #233

* Add additional example manuscripts & citations

* Update frozen references

* Switch raw:dongbo-conversation to raw:paywall-movie. Now appears as:
21. Paywall: The Business of Scholarship [Internet]. 2018. Available:
https://paywallthemovie.com/paywall

Fixing of individual references as follows:

* Fix math in reference title for doi:10.1103/physrevlett.114.191803
use title from https://www.ncbi.nlm.nih.gov/pubmed/26024162

* Update Kipoi citation
Preprint has been published.

* Remove errant DOI for https://hdl.handle.net/10261/160086

* Update Silva et al from preprint to mSphere DOI

* Add book publisher place
dhimmel added a commit to dhimmel/meta-review that referenced this issue Jul 9, 2019
@dhimmel
Harden shell scripts with improved robustness & verbosity (greenelab#233
ddb0288 
)

Merges manubot/rootstock#233

Hat tip to Michael Hoffman (https://hoffmanlab.org/) for feedback.

* Apply shell best practices
References:
https://kvz.io/blog/2013/11/21/bash-best-practices/
https://www.davidpashley.com/articles/writing-robust-shell-scripts/
manubot/rootstock#233 (comment)

* Specify bash (not just sh). Other shellcheck suggestions
Properly use command substitution and parameter expansion in the
appropriate places.

* echo diagnostic messages to stderr
Previously echo defaulted to stdout
https://stackoverflow.com/a/41766832/4651668
Placement of stderr redirect to: "echo >&2"

* Update bash options: xtrace specified by calling command

* Quote variable names

* deploy.sh: use Travis env vars for CI build URLs
These environment variables were added to Travis in late 2018
travis-ci/travis-ci#8935 (comment)
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Switch citations to PLOS Comp Bio style dhimmel/meta-review
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