====== Wiki Syntax ======

For documenting with a DokuWiki you will need to learn some basic syntax with which you can format your text documents. We have summarized the most important options  for you here. If you want additional options you can look at the complete syntax summary [[wiki:syntax||here]].

==== Headings ====

Within a page, you can organize the information using headings of different levels, just think of chapters, sections, subsections, and paragraphs. By default, headings up to level 3 will be included into the table of contents that is shown at the top of the page. The syntax to generate a heading is simple. A level 1 heading (top level) is generated by placing your heading text between two runs of six equal signs

<code>
====== YOUR L1 HEADING ======
</code>

Lower ranking headings are generated the same way, just decrease the number of equal signs. Please make sure, that your headings are not too long. <hidden ThingsToRemember>

  * Headings can be used to bring structure into your text
  * Headings up to level 4 will be included into the Table of Contents
  * The WIKI syntax to generate headings is a run of equal <nowiki>(=) </nowiki> signs

</hidden>

----

==== Blocks ====

One further option to structure the information is the text format. For example, you have seen above, that we often place information into code blocks. Note, if you place text in a code block, WIKI syntax will not be interpreted, and you see the information as you have typed it. Use the following syntax

<code>
''
Enter here your text that should appear in a grey box

''
</code>

==== Links ====

Once you have spread information across different pages (and probably also across the internet), a creative use of [[https://www.dokuwiki.org/link|Links]] can make your DokuWiki a comprehensive knowledge base. We distinguish internal links, i.e. links to pages within the same DokuWiki and external links to any website. See some examples below:

  * [[:start|internal link]]<code>
[[:start|internal link]]
</code>

  * [[http://www.uni-frankfurt.de|external link]]<code>
[[http://www.uni-frankfurt.de|external link]]
</code>

  * [[wp>Acinetobacter_baumannii|interwiki link]] (link to the Wikipedia article about Acinetobacter baumannii)<code>
[[wp>wiki|interwiki link]]
</code>

==== Tables ====

Creating tables in a DokuWiki is straightforward. Cells in a table are just separated by a '<color blue>|</color>' character. If you want to indicate a cell as a header, just prepend the information with a '<color blue>^</color>' instead of the '|'.

^ ^Heading1^Heading2^Heading3|
^Row1|Value1.1|Value1.2|Value1.3|
^Row2|Value2.1|Value2.2|Value2.3|

<hidden WikiCode><code>
^   ^Heading1 ^Heading2 ^Heading3 |
^Row1|Value1.1|Value1.2|Value1.3|
^Row2|Value2.1|Value2.2|Value2.3|
</code>

</hidden>

----

==== Advantages ====

DokuWikis have a couple of advantages over traditional paper-based documentations of your work. These are, among others

  - **The DokuWiki is easy to use**
  - **Exhaustive documentation**  is possible via copy and paste
  - **Broad range of text formatting options**
  - **Extendable via [[https://www.dokuwiki.org/plugins|Plugins]]**
  - **Subordinate information can be hidden**<WRAP>
<hidden WikiCode><code>
<hidden WikiCode>
Display some information only when the user clicks on the words WikiCode
</hidden>
</code>

</hidden> </WRAP>

  - Numbered lists can<WRAP>
      - help
      - you
      - structure
      - things<WRAP>

<hidden HowToContinueNumbering> See [[:general:dokuwiki:wiki_issues#how_to_continue_a_numbered_list|HERE]] if your numbering breaks due to intervening images, code, and the like. </hidden> </WRAP>

  - exhaustively

<hidden WikiSyntax><code>
  - Numbered lists can<WRAP>
    - help
    - you
    - structure
    - things<WRAP>
<hidden HowToContinueNumbering>
See [[general:dokuwiki:wiki_issues#How_to_continue_a_numbered_list|HERE]] if your numbering breaks due to intervening images, code, and the like.
</hidden>
</WRAP>
    - exhaustively
</code>

</hidden> </WRAP>

  - **<color blue>Text formatting</color> enhances the information transfer**<WRAP>
<hidden WikiCode><code>
<color blue>Text formatting</color>
</code>

The use of

<code>
<color>...</color>
</code>

requires the plugin [[https://www.dokuwiki.org/plugin:color|color]] </hidden> </WRAP>

  - Text can be **bold face**, //italics//, **//bold face italics//** <WRAP>

<hidden WikiCode><code>
Text can be **bold face**, //italics//, **//bold face italics//**
</code>

</hidden> </WRAP>

  - **Entire code blocks (relevant for bioinformaticians) can be integrated via copy and paste**
<file bash forloop.sh>
for i in `ls`; do echo $i; done
</file>

<WRAP>

<hidden WikiCode>

<code>
<file bash forloop.sh>
for i in `ls`; do echo $i; done
</file>
</code>

</hidden> </WRAP>

  - **cross-linking of information via [[:start|internal links]] and [[http://www.dokuwiki.org|exernal links]] is simple** <WRAP>
<hidden WikiCode><code>
**cross-linking of information via [[:start|internal links]] and [[http://www.dokuwiki.org|exernal links]] is simple**
</code>

</hidden> </WRAP>

  - **organize and re-organize information using section headings, pages, and links**
  - The **Media Manager**  makes the integration of all kinds of media straightforward.
  - **Integration of Media**  into a page is straightforward (Figure {{ref>AB}}). Note, the integration of media requires that they first have been uploaded via the Media Manager.<WRAP>
<figure AB> {{:howto:abaumannii.png?200  }}<caption> EM Image of //A. baumannii//  </caption> </figure> <hidden WikiCode><code>
**media integration is straightforward** (Figure {{ref>AB}}).
<figure AB>
{{:howto:abaumannii.png?200 |}}
<caption>
EM Image of //A. baumannii//
</caption>
</figure>
</code>

</hidden> </WRAP>

  - **Information sharing among members of a working group is simple**
  - [[https://applbio.biologie.uni-frankfurt.de/teaching/wiki/doku.php?id=pbioc_basics:tasksetwiki&do=revisions|Revisions]] allow to move back to older versions of the WIKI
  - **Change history allows to monitor who changed when a particular page (see bottom right of the page)**
  - **Backups increase data security**
  - Task assignment using the [[https://www.dokuwiki.org/plugin:do|do plugin]] in combination with the [[https://www.dokuwiki.org/plugin:sqlite|sqlite plugin]]<WRAP>

<do 2035-05-30 ingo>Retire</do><WRAP> <hidden Code><code>
<do 2035-05-30 ingo>Retire</do>
</code>

</hidden> </WRAP>

  - Placing text with an indent<WRAP>

<wrap indent>This is the indented Text</wrap> <hidden WikiCode>

<code>
Placing text with an indent<WRAP>
<wrap indent>This is the indented Text</wrap>
</WRAP>
</code>

</hidden> </WRAP>

Obviously, we can show here only a small set of the things that can be done with a DokuWiki. For a more comprehensive overview of the wiki syntax follow this [[:wiki:syntax|LINK]]. Feel also free to search the available [[https://www.dokuwiki.org/plugins|plugins]] for further inspirations of how to extend the functionality of a [[https://www.dokuwiki.org/dokuwiki|dokuwiki]].

----

==== Disadvantages ====

Of course, there are also few drawbacks that come along with using a WIKI

  * **You need a computer, and when you access a WIKI via the web, you need an active internet connection**
  * **Unsaved changes**  will be lost once you leave the page (or the computer crashes)
  * **Web-based access**  represents a security risk
  * **WIKI-set up**  not straightforward for everybody
  * If you mix editing with the simple DW editor (you have to write the wiki syntax on your own) and with the CKG editor (this is an editor that looks a bit like what you are used to when working with MSOffice), DokuWiki can do funny things. Essentially, it can start to mix the Wiki syntax, which is considerably easy to learn, with way more complex html code.