Using Microsoft Word

It’s not a typewriter!

Layout hasn’t changed much...

Gutenberg Bible (Raul654 2005)

Goals

• What to Do– Standard formatting conventions– Best Practises for Layout

• How to Do It– Tools available in Word– Save time & effort when making documents

• To make documents of high quality

Compatibility

• Word 6.0 and all subsequent versions– Both Windows and Macintosh– Commands are in different places– Terminology is the same

• OpenOffice Writer– Equivalent features– Terminology occasionally different

• Papers (iWork) and WordPerfect– Analogous features...somewhere

Anatomy of a PageHeader

Body

Footer

Header

Body

Footer

Verso (Even) Recto (Odd)

Margin

Margin

Margin

Margin

Gutter

Fonts

• Serif or Roman Font– Use for body text and captions– Examples: Times New Roman, Bookman

• Sans Serif Font– Use for titles, headings, on-screen text, captions/caption

labels, maybe body text– Examples: Calibri, Arial, Verdana

• Slab Serif, Typewriter, or Monospaced Font– Use for computer commands, URLs, sequence data– Examples: Courier New, Lucida Sans Typewriter

Font Styles• Classical

– Humanist (e.g., Centaur, Bookman Old Style)– Garalde (e.g., Garamond)– Transitional/Realist (e.g., Times Roman)

• Modern– Didone (e.g., Bodoni, Cambria)– Mechanistic (e.g., Courier, Consolas, Inconsolata)– Grotesque (e.g., Franklin Gothic)– Neo-Grotesque (e.g., Helvetica/Arial)– Geometric (e.g., Futura, Eurostile, Century Gothic)– Humanist (e.g., Calibri, Optima, Tahoma)

• Only use Classical, Didone, or some Modern Humanist fonts for body text

Evil Fonts

• Any font which is not obviously classifiable into the above should never be used– Especially Comic Sans MS– Also Curlz MT– And Brush Script MT– These are either Novelty or Calligraphic fonts

• Never use more than 3 fonts– One for body text– One for headings and titles– One slab serif font, if required– If you are using a Modern Humanist sans-serif body text, you still

get a different one for headings, if desired

Anatomy of a Document• Title Page• Front Matter

– Page numbers are Roman numerals from 2– Made of unnumbered sections (and subsections)– Includes Table of Contents, List of Figures, List of Tables, Abstract, Executive

Summary, Revision History• Main Matter

– Page numbers are Arabic numerals from 1– Made of numbered sections (and subsection), maybe chapters– Includes Introduction, and Conclusion

• Back Matter– Page numbers can follow main matter or be per-appendix– May contain lettered appendices– Includes special unnumbered sections: Index, Glossary, References

Formatting Sections• Each section starts with a title

– The title should be in a sans-serif font– All sections except the Table of Contents should appear in the Table of

Contents• There is a collection of paragraphs

– The first paragraph must not be indented, but subsequent paragraphs must be indented

– A section must have at least one paragraph– There should be space between paragraph, but not a blank line

• There may be subsections– The formatting of the title should be slightly different– Section numbers should be hierarchical– Unnumbered sections should not have subsections

Sections and Section Breaks

• Word’s concept of sections does not match the documents concept of sections!

• Each section may have special formatting– Different header and footer– Change in page number start and format

• Section Breaks separate sections– Next page– Next odd page (for chapters)

Presentation versus Semantics

1 INTRODUCTIONSince detecting orthologs, genes diverging after speciation events, can be time consuming if done using phylogenetic trees, researchers have devised shortcuts, or working definitions, such as that of reciprocal best hits. Beyond the fact that orthology is not transitive

Presentation: 18pt VerdanaSemantic: 1° Section Header

Presentation: 12pt Times New RomanSemantic: Body Paragraph

Styles

• Styles apply formatting to text– Avoid repetitive formatting

• Create styles with semantic means– Examples: Section Header, Species Name, Gene Name

• Styles:– Automatically reformat all instances when changed– Come in 3 flavours

• Character (In-line bits of text)• Paragraph (Blocks of text)• Linked (Both)

– Inherit the properties of another style– Can suggest the style of the next paragraph

Bold, Italic, and Underline• Italic is used for

– Emphasis (e.g., I really need to use the bathroom.)– Unusual words (e.g., we can define a monoid over the category of endofunctors.)– Species names (e.g., R. leguminosarum biovar viciæ strain 3841)

• sp., subsp./subspecies, bv./biovar, sv./serovar, mv./morphovar, and strain are never italicised

• Bold is used for– Titles– Keywords

• SMALL CAPS is used for– Titles– Some computer text (e.g., PERL is preferred to perl, PERL, or Perl and bash or BASH are preferred to

BASH)• Oblique, if your font has it, is interchangeable with italic

– Useful for avoiding confusion (e.g., E. coli has many pathogenicity islands.)• Avoid combining them, especially for extra emphasis

– It looks cheap• Check that formatting does not include external punctuation (this is ugly)• Never use underline, shadow, emboss, and engrave or strikethrough

Space

• Neither one nor two spaces after a period is correct– One space is called “French spacing”

• Numbers should be separated from units by a thin space– 10 kg, not 10 kg; 500 m/s², not 500 m/s²

• Abbreviations should be followed by a non-breaking space– Dr. Guinel, never Dr.

Guinel

Commas and Quotes

• Commas always appear after e.g. and i.e.– (e.g., a book) is (for example, a book)– (i.e., a book) is (that is, a book)– Rarely in italics

• Quotes can be curved or straight– Use straight quotes for computer things– Use “ or ‘ at the start of a quotation and ” or ’– Put a thin space between nested quotes (e.g., “ ‘Interesting’ was all

she said,” Paul retorted.)– Apostrophes are always ’ (e.g., the ’80s, not the ‘80s)– Grace (`) is not used in English (on the same key as ~)– Prime (′) for chemicals and mathematics (e.g., the 3 hydroxyl, ′ f (′ x))

Ligatures

• Ligatures are linked letters (e.g., encyclopædia)• Some people consider them archaic• Phonetics-dependent ligatures are inserted manually

– æ is usually written ae in British English or collapsed to e in American English

– œ is usually written oe in British English or collapsed to e in American English (e.g., œstrogen, oestrogen, estrogen)

– Latin follows separate rules, usually favouring the ligature• Typographic ligatures are automatically converted

– e.g., ff → ff, fi → fi, fl→ fl, ffi → ffi, ffl → ffl, and, rarely, others– Word now automatically uses ligatures; PowerPoint does not

Look-alikes• ß is a ligature in German for ss (e.g., strasse → straße)

• Do not confuse it with the Greek β• ß-sheet is a sssheet

• Product(∏) and Sum(∑) are different from the Greek Pi(Π) and Sigma(Σ)• Four different horizontal lines!

– Hyphen (-) for separating words– Minus (−) for math– En dash (–) for separating ranges– Em dash (—) for interrupting sentences

• There are old approximations that now have characters– Tilde(~) was used for Almost Equal(≈)– The digraph >= was used for Greater Than or Equal To (≥)– The digraph =< was used for Less Than or Equal To (≤)– The digraph == was used for Identical To (≡)– Any of /=, =/=, or != were used for Not Equal To (≠)

• When in doubt, browse Insert Symbol, search online for “Unicode symbol for…” or check the Wikipedia

Justification

• Left Justified, Flushed Left, Ragged RightAs for you who stand today on the threshold of life, with a long horizon open before you for a long career of usefulness to your native land, if you will permit me, after a long life, I shall remind you that already many problems rise before you: problems of race division, problems of creed differences, problems of economic conflict, problems of national duty and national aspiration.

• Justified, Fully Justified, Block JustifiedAs for you who stand today on the threshold of life, with a long horizon open before you for a long career of usefulness to your native land, if you will permit me, after a long life, I shall remind you that already many problems rise before you: problems of race division, problems of creed differences, problems of economic conflict, problems of national duty and national aspiration.

• Justified with Hyphenation

Fields

• Automatically generated text• Used for table of contents, list of figures, list of

tables• Allows you to create cross-references• Requires that you use styles• Occasionally need to Select All → Update

Fields

Graphics• Vector graphics describe a drawing

– “Infinite” resolution (no jaggies)– Easy to modify– Built-in drawing tools, Adobe Illustrator, Inkscape– Embedded Office objects (e.g., Excel graphs) are always vector graphics

• Raster graphics are a bunch of pixels– JPEG compression introduces colour distortions (artefacts) and should

only be used for photos– PNG should be used for images with solid colours

• PNG can also include transparency

• Vector graphics can include bitmaps– e.g., create a labelled photo as a vector graphic

Graphics (Examples)

JPEGPNGVector

Drawing Tools• Heatmaps

– R• Data Plots

– gnuplot– R– Microsoft Excel

• Equation Plots– gnuplot– R

• Phylogenetic Trees– Rooted

• DrawTree (PHYLIP)

– Unrooted• DrawGram (PHYLIP)• TreeGraph2

• Networks– Directed

• Dot (GraphViz)

– Undirected• Neato (GraphViz)• Cytoscape

– Processes• Dot (GraphViz)• Microsoft Visio• Inkscape/Adobe Illustrator

• General Vector Graphics– Inkscape – Adobe Illustrator– Microsoft Word (painful)

• Photo retouching– GIMP– Adobe Photoshop

Referencing

• Word 2007 has a citation manager– Limited styles– Community style bank: http://bibword.codeplex.com

• Must populate the document with reference information– Not presently easy– Word cannot import title/author/journal from PubMed,

DOI, or Arxiv identifiers or PDFs– Most existing citation managers will not export to Word– Ugly conversion toolkit available:

http://www.scripps.edu/~cdputnam/software/bibutils/

Bonus: PowerPoint

• All the stuff about graphics and fonts applies!• Use only 2 fonts

– 1 sans serif– 1 slab serif, if needed

• Styles are built into the Themes settings– Use the Master slide to apply graphics on every slide

• Use colour sparingly– Black and white is boring– A significant number of people are red-green colour blind

• Use animation only to illustrate a process– Don’t animate slide transitions or text, ever!– Don’t include sound effects

LATEX• LATEX is a document preparation system

– Bibliography manager with multiple styles– Multi-file documents– Index manager– Produces PDF output

• Not WYSIWYG; Uses markup– e.g., pK19mob\,sacB was cut using \textit{Eco}RI.

• Package system– biocon for typesetting species names– texshade for typesetting alignments

• Macros possible– Make repeated commands simple– e.g., \Eri → EcoRI

• Steep learning curve, but very worth it for large documents

Demonstration

• Reformat Emily’s master’s proposal• Get a copy at http://kuum.wlu.ca/bi296.doc• Reference guide on http://jasonpang.net/• This presentation available at

http://www.masella.name/~andre/UsingWord.pptx• Ask about my WLU+UW vector graphics pack