# Help:Contents

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Here are some instructions on using ChoanoWiki. The syntax is essentially the same as wikipedia. Another good way to learn is to use existing pages as examples---click the 'edit' link at the top of a page to see the source. If you have any problems with the wiki, you can email me at: markdayel@gmail.com

# Wikitext Formatting

You can find info on how to format wikitext here. Below are some commonly used examples with their wiki code.

To create a new page, first make a link to it in an existing page, by enclosing text in double square brackets, e.g.:

[[Choanoflagellates]]

Then click on the new link to create the new page.

You can change the link text by putting a vertical bar between the page title and the link text (try to keep the actual page titles short, and text only (no symbols like '?')):

[[Choanoflagellates|What are Choanoflagellates?]]

External links have only one set of brackets, and have a space not a vertical line between the link and the link text:

[http://www.wikipedia.org/ Wikipedia]

### Common Formatting

Emphasizing text:

bold italic
 '''bold'''  ''italic''

Superscripts and subscripts:

x2, H2O
 x<sup>2</sup>, H<sub>2</sub>O

Surround text with '=' signs to signify titles. The fewer, the bigger the title:

# Title1

## Title2

### Title3

#### Title4

=Title1=
==Title2==
===Title3===
====Title4====


Indent lines with colons:

indent
moreindented
even more
:indent
::moreindented
:::even more


Begin lines with * or # for point or numbered lists

• Point
• Point
1. Number
2. Number
1. Number Under Number
3. Number
• Point Under Number
*Point
*Point
#Number
#Number
##Number Under Number
#Number
#*Point Under Number


# DNA sequences

000001 ATGACTGACA CACTGATAGC TACGATCtag ctagcatgct acgatgctag catgctagct 000060
000061 gac
<dnaseq>ATGACTGACAC ACTGATAGCTACGATCtagctagcatgctacgatgctagcatgctagctgac</dnaseq>

# Citations

We can cite choano books and papers by PMID or ISBN [1, 2], or write out the citation explcitly[3].

#### References

1. isbn:1-4367-3924-1. [savillekent1882]
2. FJERDINGSTAD EJ. Ultrastructure of the collar of the choanoflagellate Codonosiga botrytis (Ehrenb.). Z Zellforsch Mikrosk Anat 1961; 54 499-510. pmid:13700095. [fjerdingstad1961]
3. Choanos are great!

[choanosgreat]

We can cite choano books and papers by PMID
or ISBN <cite>savillekent1882 fjerdingstad1961</cite>,
or write out the citation explcitly<cite>choanosgreat</cite>.

==== References ====
<biblio>
#savillekent1882 isbn=1-4367-3924-1
#fjerdingstad1961 pmid=13700095
#choanosgreat Choanos are great!
</biblio>


You can also import Endnote libraries: http://openwetware.org/wiki/Wikiomics:Biblio#Integration_with_Endnote

## Maps

You can include maps (via Google Maps). This page contains instructions and links to two video tutorials. Here's an example:

Produced with this code:

<googlemap version="0.9" lat="37.452783" lon="-75.675216" zoom="11" scale=yes controls=small>
37.452783,-75.675216
Proterospongia Collection Site: 37.452783N 75.675216W, off Hog Island, Virginia, US
</googlemap>

# Math

Math formatting (in LaTeX) also works:

$\begin{bmatrix} \vec{y} \\ 1 \end{bmatrix} = \begin{bmatrix} A & \vec{b} \ \\ 0, \ldots, 0 & 1 \end{bmatrix} \begin{bmatrix} \vec{x} \\ 1 \end{bmatrix}$
$\vec{y} = A \vec{x} + \vec{b}.$
:$\begin{bmatrix} \vec{y} \\ 1 \end{bmatrix} = \begin{bmatrix} A & \vec{b} \ \\ 0, \ldots, 0 & 1 \end{bmatrix} \begin{bmatrix} \vec{x} \\ 1 \end{bmatrix}$
:$\vec{y} = A \vec{x} + \vec{b}.$

# Uploading Files

Upload files with the 'Upload file' link on the left. You can upload image files, pdfs, movies etc. Avoid uploading images as tif format if possible since it is not natively supported by most browsers and produces huge files (png is a good lossless format if you want the image to have perfect accuracy, otherwise jpeg with quality of 95% works very well and produces relatively small files)

There is a limit on the upload file size. If you want to upload something really big, email me: markdayel@gmail.com

Media files can be linked to in the text with e.g.

[[:media:mypaper.pdf | here's my paper]]

Images can be typeset with thumbnails automatically, e.g.

[[Image:Choanodiagram3.1.jpg|thumb|250px|right|Choanoflagellate]]

will produce a 250 pixel wide thumbnail of the image on the right of the page, with the caption 'Choanoflagellate'

Wiki table formatting is a bit byzantine---to quickly convert tables from excel to wikitext, you can use this online form but please also upload the xls file to make it easier for others to update the table.

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