(r10) Barrick Lab :: Manuscript Style Guide

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---+ Barrick Lab Style Guide

---++ Writing a Scientific Paper

   * [[http://cgi.stanford.edu/~dept-ctl/cgi-bin/tomprof/posting.php?ID=1176][Twenty Steps to Writing a Research Article]] (Tomorrow's Professor Mailing List Archive #1176)

---++ General Formatting

   * Use a single space after a period between sentences.
   * Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
   * Manuscripts should generally be double spaced throughout.
   * For most manuscripts, it's not a bad idea to put a simple page number centered at the bottom of each page.

---++ 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.
   * To add italics to species names in downloaded citation titles, add HTML italics tags around them.
      * e.g. Escherichia coli to &lt;i&gt;Escherichia coli&lt;/i&gt;
   * 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 <nop>PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
   * 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]].
   * Correct article titles so that only the first word and proper nouns are capitalized.
      * Also capitalize words after colons in the title.

---++ 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 other formats 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) |

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 names have the IS in normal font and the following number italicized (IS<i>1</i> and IS<i>150</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
Contributors to this topic
JeffreyBarrick
Topic revision: r10 - 2013-08-13 - 14:05:15 - Main.JeffreyBarrick