(r14) Barrick Lab :: Manuscript Style Guide

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---+ Barrick Lab Style Guide

---++ Writing a Scientific Paper

   * [[https://www.unl.edu/gradstudies/connections/twenty-steps-writing-research-article][Twenty Steps to Writing a Research Article]] (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and Ethics Program, University of Pittsburgh)

---++ General Formatting

   * Manuscripts should generally be double spaced throughout.
   * Don't format with multiple columns.
   * Use a single space after a period between sentences.
   * Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
   * Add a page number. Usually centered at the bottom of each page.
   * Many journals encourage adding line numbers to aid in review.

---++ Citations

   * Use [[http://www.mendeley.com/download-mendeley-desktop/][Mendeley]] to organize your citations and insert them into word processing documents.
   * If you aren't formatting for submission to a specific journal, use the __Nature Reviews Genetics__ style.

---+++ Tips for Working with Mendeley
It can be difficult to get citation management software to output bibliographies with precisely the right formatting. Here are some tips for working with Mendeley to get exactly what you want.

   * If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in [[http://www.pubmed.com][PubMed]], copy the Digital Object Identifier (DOI) and/or the <nop>PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
      * Annoyingly, you may have to manually correct any cases where the initial "a" is present in an author's name to be uppercase after importing!
   * Correct article titles so that only the first word and proper nouns are capitalized.
      * Also uncapitalize words after colons in the title. "This is the title: how to do it". Normal style is to only capitalize the part after a title if it is a complete sentence (independent phrase). "How to write titles: This is how to do it".
   * To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
      * e.g., Escherichia coli to &lt;i&gt;Escherichia coli&lt;/i&gt; = _Escherichia coli_
   * To add Greek letters or other symbols, you can also add HTML tags.
      * e.g., beta to &amp;beta; = &beta;
   * For citing a publication from a consortium (example R Core team), you can suppress the normal First Name MI Last Name formatting by Mendeley by clicking on the name with (Institution/Organization) after it in the drop-down menu after you enter it in the author box.
   * Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses *article numbers*. Fix the starting page to be the *article number* and delete the ending page so it is blank.
   * You can prevent the HTML links to articles from appearing after each bibliography entry by going to > Citation Style > More Styles and changing the "Include URLs" menu setting.
   * To enable using journal abbreviations follow these directions:
      1 Open the Mendeley Desktop user data folder by pressing Cmd+Shift+D (Mac) and clicking 'Open Data Directory'.
      2 Create a folder inside the Data Directory called "journalAbbreviations".
      3 Within this folder, create a plain text file called "default.txt". Each line in this file is a full journal title followed by a tab and then the abbreviation to substitute for this journal title. Matching of the journal title is case-sensitive. 
         * You can download a version of this file that should contain most common abbreviations [[%ATTACHURL%/default.txt][here]].
      4 If an entry does not exist in this file, you can find the standard abbreviation using [[http://cassi.cas.org][CAS]] or [[http://www.library.illinois.edu/biotech/j-abbrev.html][other resources]].

---++ Figures and Graphs

   * Create figures in a vector graphics program (e.g., Adobe Illustrator).
   * Always include a legend for symbols within a figure, NOT just in the figure caption.
   * Unlike the defaults in Microsoft Excel:
      * Enclose the data frame of a graph in a full box.
      * Generally, do not include any grid lines on graphs.
      * Do not use shadow effects.
   * Use 95% confidence intervals, rather than standard deviations for error bars.
   * Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

---++ Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this table.

%TABLE{dataalign="left,center,left"}%
| *Name* | *Symbol* | *Do not use...* |
| prime | &prime; | ' (single quote) |
| times | &times; | x (letter x) |
| degrees | &deg; | <sup>o</sup> (superscript zero) |

Here are some websites that contain many more unicode symbols: %BR%
Main: [[http://www.alanwood.net/unicode/][Unicode Website]] | [[http://www.alanwood.net/unicode/search.html][Search]] %BR%
Groups of symbols: [[http://www.alanwood.net/unicode/general_punctuation.html][Punctuation]] | [[http://www.alanwood.net/unicode/arrows.html][Arrows]] | [[http://www.alanwood.net/unicode/miscellaneous_mathematical_symbols_a.html][Math]]

---++ Scientific Conventions

   * Use the prime symbol, not a single quote (see above) for DNA's 5&prime; and 3&prime; ends.
   * For microbes, gene names are italicized (<i>lasT</i>) and their protein products are capitalized and not italicized (<nop>LasT).
   * Insertion sequence and transposon names have the IS/Tn in normal font and the following number italicized (IS<i>1</i>, IS<i>150</i>, Tn<i>7</i>).
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
txt	default.txt	r1	manage	958.8 K	2013-02-03 - 15:22	JeffreyBarrick	Mendeley journal abbreviation file
Barrick Lab > ProtocolList > ProtocolsStyleGuide
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JeffreyBarrick
Topic revision: r14 - 2020-11-24 - 13:20:01 - Main.JeffreyBarrick