(r8) 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.

---++ 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.
   * You will generally need to manually correct the journal names from downloaded papers to their standard abbreviations. 
      * e.g. _Journal of Bacteriology_ to _J. Bact._
      * 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 website.

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]]
Barrick Lab > ProtocolList > ProtocolsStyleGuide
Topic revision: r8 - 2013-01-10 - 16:31:34 - Main.JeffreyBarrick