Banana Slug Genomics

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====== Style guide ======

Please use the following **style guide** when creating and maintaining article pages on this wiki.

===== Syntax reference =====
Refer to the [[wiki:syntax|DokuWiki syntax guide]] for any questions regarding formatting syntax.

As an introduction, Andreas Gohr has a couple of short DokuWiki video tutorials at, 
[[http://www.splitbrain.org/blog/2008-10/05-dokuwiki_beginners_screencast_01|DokuWiki Beginners Screencast #1 and #2]].   --- //[[jlong@soe.ucsc.edu|Jeff Long]] Tue Mar 30 13:45:05 PDT 2010//

===== Articles =====

==== Title ====
When creating an article title, please keep the following guidelines in mind:
  * Only capitalize the first letter in the title as you would in a normal sentence. Exceptions include, but are not limited to, capitalizing proper nouns and capitalizing names.
  * Please try to keep the article title short in length, preferably no more than 10 words in length.
  * Avoid the use of any special characters, unless the characters are a part of a proper noun or name.
Please use headline level 1 formatting when creating the article title, as illustrated in the syntax below:

<code>
====== Article title ======
</code>

==== Sectioning ====
When creating a new section for an article, use the following guidelines:
  * As with the article title, only capitalize the first letter of the section heading. Exceptions include, but are not limited to, capitalizing proper nouns and capitalizing names.
  * Keeping section headings unique within any given article is strongly preferred.
  * A blank line before the section heading is required for the sake of readability when editing.
Sample headline levels for use in section headings are given below:

<code>
===== Headline level 2 =====
==== Headline level 3 ====
=== Headline level 4 ===
== Headline level 5 ==
</code>

==== Table of contents ====
When three or more headlines are used on a given page, a table of contents is automatically generated. Headline levels 3 or greater are not included in the table of contents.

===== Formatting =====

==== Bold ====
Use boldface when:
  * referring to the article title in the opening paragraph of an article.
  * using definition lists.
Boldface text is created by surrounding text with two asterisks on both sides. Refer to the following syntax:

<code>
Here is some sample **boldface text**.
</code>

==== Italics ====
Use italics when referring to genera and all lower taxa, as well as gene names. Italicized text is created by surrounding text with two forward slashes on both sides. Refer to the following syntax:

<code>
In BME 235, we will be working with the //Ariolimax dolichophallus// genome.
</code>

==== Underline ====
Underlined text is created by surrounding text with two underscores on both sides. Refer to the following syntax:

<code>
Here is some sample __underlined text__.
</code>

==== Subscript ====
Subscript is created by surrounding text with "sub" tags. Refer to the following syntax:

<code>
The chemical formula for water is H<sub>2</sub>O.
</code>

==== Superscript ====
Superscript is created by surrounding text with "sup" tags. Refer to the following syntax:

<code>
Here is some sample <sup>superscript</sup>.
</code>

===== Images =====
When adding images to an article, refer to the following guidelines:
  * Images should be located within the section with the content related to the image.
  * Add captions as [[wp>Alt_attribute]] as a description to accompany an image whenever possible.
  * Try to avoid cramming text between two adjacent images.
Use the following syntax to insert images into an article:

<code>
Internal vs. external images:
internal
{{wiki:my_image.png}}
external
{{http://www.dokuwiki.org/_media/wiki:dokuwiki-128.png}}

Sizing images:
full size
{{wiki:my_image.png}}
given width in pixels
{{wiki:my_image.png?50}}
given width and height in pixels
{{wiki:my_image.png?200x50}}

Aligning images:
left align
{{ wiki:my_image.png}}
right align
{{wiki:my_image.png }}
center align
{{ wiki:my_image.png }}

Caption:
alt attribute with centered image
{{ wiki:my_image.png |Here is a caption as an alt text.}}
</code>

===== Tables =====
Use the following syntax to insert a table into an article:

<code>
^ Heading 1      ^ Heading 2       ^ Heading 3          ^
| Row 1 Col 1    | Row 1 Col 2     | Row 1 Col 3        |
| Row 2 Col 1    | Some colspan (Note the double pipe!) ||
| Row 3 Col 1    | Row 3 Col 2     | Row 3 Col 3        |
</code>

The sample syntax above would create the following table:

^ Heading 1      ^ Heading 2       ^ Heading 3          ^
| Row 1 Col 1    | Row 1 Col 2     | Row 1 Col 3        |
| Row 2 Col 1    | Some colspan (Note the double pipe!) ||
| Row 3 Col 1    | Row 3 Col 2     | Row 3 Col 3        |

Be sure to use the same number of separators (carats or pipes) for the number of columns for each row. Whitespace between content and separators is strictly not required, but allows for easier readability. For further table formatting details, please refer to the [[http://www.dokuwiki.org/syntax#tables|DokuWiki syntax guide for tables]].

===== Bulleted and numbered lists =====
When deciding if it is appropriate to use a list, please keep the following guidelines in mind:
  * If the information is more easily read in paragraph format, do not use a list.
  * Use a numbered list only if the sequence of items in the list is necessary or you need to reference the items in the list.
  * If a numbered list is not required, use a bulleted list.

==== Bulleted lists ====
A bulleted list is created by indenting the text by two spaces and using an asterisk for the list element. Refer to the syntax below:

<code>
An unordered/bulleted list:
  * List element 1
  * List element 2
  * etc.
</code>

==== Numbered lists ====
A bulleted list is created by indenting the text by two spaces and using a dash for the list element. Refer to the syntax below:

<code>
An ordered/numbered list:
  - List element 1
  - List element 2
  - etc.
</code>

===== Links =====
When creating hyperlinks to be added to an article, use the following guidelines:
  * Only make links where they would be relevant to the context.
  * Double check links when you are done - make sure the link goes to where you intended.

==== Internal links ====
When adding a hyperlink to another page within the wiki, use the following syntax:

<code>
[[pagename]]
or
[[pagename|link text]]
</code>

==== External links ====
When adding a hyperlink to a page external to the wiki, use the following syntax:

<code>
[[http://www.ucsc.edu]]
or
[[http://www.ucsc.edu|University of California, Santa Cruz]]
</code>

==== Interwiki links ====
When adding a hyperlink to a wiki page external to the wiki, use the following syntax:

<code>
For Wikipedia:
[[wp>Main_Page]]
</code>

Refer to the [[doku>Interwiki]] page for a list of different websites that you can use with Interwiki links.

===== Citations =====
Basic citations can be done with footnotes. Use a set of double parenthesis in order to create a footnote, as illustrated in the following syntax:
<code>
Here is a sample sentence.((Place citation here))
</code>

Footnotes are automatically numbered and linked in DokuWiki.

 --- //[[cbrumbau@soe.ucsc.edu|Christopher Brumbaugh]] 2010/04/02 08:25//

====== In Progress ======

We need to decide on and implement an official format for citations; using footnotes is "totally lame". Any suggestions?  --- //[[learithe@soe.ucsc.edu|Jenny Draper]] 2010/03/30//

I can install various plugins for citation formatting: [[http://www.dokuwiki.org/plugins?plugintag=references]].  What do people think would work best? --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/03/30 15:40//

[[http://www.dokuwiki.org/plugin:refnotes|refnotes]] seems the  most promising option. There's also [[http://www.dokuwiki.org/plugin:cite|cite]], but its description is very vague. Too bad the [[http://www.dokuwiki.org/plugin:bibtex|bibtex]] one has a reported and unpatched major vulnerabilty.  --- //[[learithe@soe.ucsc.edu|Jenny Draper]] 2010/03/30 16:04//

It looks like the [[http://www.dokuwiki.org/plugin:refnotes|refnotes plugin]] should be sufficient for assisting in formatting the citations needed for the wiki. The [[http://www.dokuwiki.org/plugin:cite|cite plugin]] allows easy citation of pages on the wiki that the plugin is installed on and as such probably would not help with citation formatting. I have found the [[http://www.dokuwiki.org/plugin:imagereference|imagereference plugin]] that allows MediaWiki style (e.g. Wikipedia) captions for images; this would be significantly better than just using alt text for captions. What style should we use for the citing references on the wiki? --- //[[cbrumbau@soe.ucsc.edu|Christopher Brumbaugh]] 2010/04/02 08:04//
Banana Slug Genomics

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