Barrick Lab :: Manuscript Style Guide

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---+! Barrick Lab Style Guide

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---++ 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.
   * Don't indent the first paragraph after a heading.
   * Add a page number. Usually centered at the bottom of each page.
   * Many journals encourage adding line numbers to aid in review.

---++ Citations

   * Use [[https://www.zotero.org/][Zotero]] 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.
   * Be sure you are using standard journal abbreviations. You can find them by Googling and looking for: "Abbreviated title (ISO 4)".

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

   * 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 switch the normal First Name MI Last Name formatting by clicking on the rectangular box to with right of the author name.
   * 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.

---++ Figures and Graphs

   * Create figures in a vector graphics program (e.g., Adobe Illustrator).
   * Always include a graphical legend for symbols within a figure, NOT just in the figure caption.
   * Don't include the written figure caption in the figure file. Include it in the manuscript.
   * Unlike the defaults in Microsoft Excel and/or ggplot2:
      * Enclose the data frame of a graph in a full box.
      * Generally, do not include any grid lines on graphs, except major reference lines (e.g., zero, control, or wild-type values for comparison).
      * 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 _extremely_ careful to not change the locations of data points or error bars relative to axis ticks during this process!!)

---++ Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform and if you need to change the font of a document. 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) |
| minus sign | &minus; | - (hyphen) |
| degrees | &deg; | <sup>o</sup> (superscript zero) |
| micro sign | &micro; | u (the letter u) |

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 for DNA's 5&prime; and 3&prime; ends (see Symbols section above).
   * Separate number from units with a space: 200 &micro;L, not 200&micro;L.
   * For microbes, gene names are italicized (<i>pykF</i>) and their protein products are capitalized and not italicized (<nop>PykF).
   * 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>).
   * Promoter names are often a capital "P" followed by a subscript name of the gene they were taken from (in italics) or a name such as for synthetic promoters from the iGEM registry (not in italics). Less often they are a capital "P" followed by lowercase letters. (Preferred: P<i><sub>yijC</sub></i>, P<sub>J23100</sub>, P<sub>CP25</sub>; OK: Ptac).
   * Plasmid names should start with a lowercase "p" and then a designation consisting of uppercase letters and numbers. It is best practices for this to be the initials of a researcher or collection followed by a numeric index (pBTK800, pJEB11, pUC19).

---++ Further Reading

   * [[https://journals-asm-org/nomenclature][ASM Nomenclature Guidelines]] - includes information on naming mutations and alleles.
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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
This topic: Lab > WebHome > ProtocolList > ProtocolsStyleGuide
Topic revision: r18 - 2023-12-26 - JeffreyBarrick