User:Bradley Monk

New-ish Pages

• PhD Demographics
• Actin
• TYRO3

CUSTOM WIKI EDITING TOOLBAR

To customize the wiki editing toolbar, GO HERE (User:Bradley_Monk/common.js)

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CSS & JS

• global.js
• Special:MyPage/common.js

Mediawiki Extensions

• Help:Link_color
• Extension:Semantic_Forms
• Extension:Popups

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MediaWiki Help Pages

• [MediaWiki Markup]
• Category:Templates
• OneSci Help
• Mediawiki Markup Images
• MediaWiki Magic Words
• MediaWiki Tables
• MediaWiki ImageAnnotator
• Mediawiki References
• Math
• Template Tips
• Advanced Templates
• Transclusion

Bradleymonk.com .JS

• MediaWiki:Common.js
• MediaWiki:LAPI.js
• MediaWiki:Gadget-ImageAnnotator.js
• MediaWiki:ImageAnnotatorConfig.js
• MediaWiki:LAPI.js
• MediaWiki:TextCleaner.js
• MediaWiki:Tooltips.js
• MediaWiki:UIElements.js
• MediaWiki:AjaxSubmit.js

HTML & CSS

• Manual:CSS

  MediaWiki:Common.css

• Manual:Skin_configuration
• Manual:Skinning
• Help:Skins

Adding HTML5 Video to MediaWiki

To embed a youtube video, use the following code:

{{#ev:youtube|tDKUU0SqbSA}}

{{#ev:youtube|tDKUU0SqbSA}}

Extension LinkTitles

AUTO GENERATED SITE LINKS

• MediaWiki Extension Page

require_once( "$IP/extensions/LinkTitles/LinkTitles.php" );
$wgLinkTitlesSmartMode = false;         // false = case sensitive
$wgLinkTitlesMinimumTitleLength = 7;    // default is 3
$wgLinkTitlesSkipTemplates = true;      // skip any text in a {{template|text}}
$wgLinkTitlesFirstOnly = true;          // only link the first occurrence
$wgLinkTitlesBlackList = array();
$wgLinkTitlesBlackList[] = 'MediaWiki';
$wgLinkTitlesBlackList[] = 'mediaplayer';

USE THE __NOAUTOLINKS__ TAG ON A WIKI PAGE TO PREVENT LINKING ON THAT PAGE

__NOAUTOLINKS__ 

__NOAUTOLINKS__

Template:SlideBox

{{SlideBox|width=80%|float=left|
Header [[Content]] Is Shown
|
Body text is hidden
}}

Header Content Is Shown

Body text is hidden

Customize Editing Toolbar

http://bradleymonk.com/User:Bradley_Monk/common.js http://www.mediawiki.org/wiki/Extension:WikiEditor/Toolbar_customization

section

• {String} (optional) The name of the section in the WikiEditor. Defaults to 'main'

id

• {String} (required) Unique id (ie. 'my-button')

icon

• {String} (recommended) URL to the icon, should be square about 21 to 22px

label

• {String} (required) Tooltip displayed when hovering button

insertBefore

• {String} (optional) Wikitext to be inserted before the cursor on-click

sampleText

• {String} (optional) Text inserted in place of the cursor if no text was selected

insertAfter

• {String} (optional) Wikitext to be inserted after the cursor on-click

callback

• {Function} (optional) Called when the button is clicked

autoSummary

• {mixed} (optional) Null or an Object with the following properties:
  • summary: {String} (required) Edit summary that should be used
  • position: {String} (optional) 'append', 'prepend' or 'replace'
  • delimiter: {String} (optional) delimiter between the (possibly) current summary and the to-be-inserted summary

Syntax Highlighting

The SyntaxHighlight extension, formerly known as SyntaxHighlight_GeSHi, provides rich formatting of source code using the <syntaxhighlight> tag. It is powered by the Pygments library and supports hundreds of different programming languages and file formats.

Usage & Parameters

<syntaxhighlight lang="python" line='line'>
def quick_sort(arr):
	less = []
	pivot_list = []
	more = []
	if len(arr) <= 1:
		return arr
	else:
		pass
</syntaxhighlight>

def quick_sort(arr):
	less = []
	pivot_list = []
	more = []
	if len(arr) <= 1:
		return arr
	else:
		pass

lang

---

The lang="name" attribute defines what lexer should be used. The language affects how the extension highlights the source code.

<syntaxhighlight lang="python">
def quick_sort(arr):
    less = []
</syntaxhighlight>

def quick_sort(arr):
    less = []

line

---

The line attribute enables line numbers.

<syntaxhighlight lang="python" line="1">
def quick_sort(arr):
    less = []
</syntaxhighlight>

def quick_sort(arr):
    less = []

start

---

<syntaxhighlight lang="python" line start="55">
def quick_sort(arr):
    less = []
</syntaxhighlight>

def quick_sort(arr):
    less = []

highlight

---

The highlight attribute specifies one or more lines that should be marked (by highlighting those lines with a different background color). You can specify multiple line numbers separated by commas (for example, highlight="1,4,8") or ranges using two line numbers and a hyphen (for example, highlight="5-7"). Note that the line number specification ignores any renumbering of the displayed line numbers with the start attribute.

<syntaxhighlight lang="python" highlight="1,5-7" start=3 line>
def quick_sort(arr):
    less = []
    pivot_list = []
    more = []
    if len(arr) <= 1:
        return arr
</syntaxhighlight>

def quick_sort(arr):
    less = []
    pivot_list = []
    more = []
    if len(arr) <= 1:
        return arr

inline

---

The attribute indicates that the source code should be inline as part of a paragraph (as opposed to being its own block).

Note that line breaks can occur at any space between the opening and closing tags unless the source code is marked non-breakable with class="nowrap" (on those wikis that support it; see below) or style=white-space:nowrap. For example:

In python, <syntaxhighlight lang="python" inline>lambda x: x * 2</syntaxhighlight> is a lambda expression.

results in:

In python lambda x: x * 2 is a lambda expression.

class

---

When inline is used, class="nowrap" specifies that line breaks should not occur at spaces within the code block.

Using class="nowrap":

<nowiki>
<div style="max-width:300px; border:1px solid #ccc "></div>
<nowiki>

xxxxxxxxxxxxxxxxxxxxxlambda x: x * 2xxxxxxxxxxxxxxx

Using style="white-space:nowrap":

<div style="white-space:nowrap; max-width:300px; border:1px solid #ccc"></div>

xxxxxxxxxxxxxxxxxxxxxlambda x: x * 2xxxxxxxxxxxxxxx

style

---

The style attribute allows CSS attributes to be included directly. This is equivalent to enclosing the block in a <div> (not <span>) tag. The tab‑size attribute cannot be specified this way; it requires an enclosing <span> tag. For example:

<div style="max-width:600px; background:rgba(10,10,10,.30);">
PYTHON:
<syntaxhighlight lang="python" style="border:1px dashed gray; background:rgba(10,10,50,.10);">
def quick_sort(arr):
	less = []
	pivot_list = []
	more = []
	if len(arr) <= 1:
		return arr
	else:
		pass
</syntaxhighlight>
</div>

PYTHON:

def quick_sort(arr):
	less = []
	pivot_list = []
	more = []
	if len(arr) <= 1:
		return arr
	else:
		pass

LaTeX Math

<math> f(x, \mu, \sigma) = \frac{1}{\sigma \sqrt{2\pi} } e^{ -\frac{(x-\mu)^2}{2\sigma^2} } </math>

$f(x,\mu ,\sigma )={\frac {1}{\sigma {\sqrt {2\pi }}}}e^{-{\frac {(x-\mu )^{2}}{2\sigma ^{2}}}}$

TeX and HTML

LIST OF MATH SYMBOLS IN HTML MARKUP

TeX Syntax (forcing PNG)	TeX Rendering	HTML Syntax	HTML Rendering
<math>\alpha</math>	$\alpha$	{{math|<VAR>&alpha;</VAR>}}	α
<math> f(x) = x^2\,</math>	$f(x)=x^{2}\,$	{{math|''f''(<var>x</var>) {{=}} <var>x</var><sup>2</sup>}}	f(x) = x2
<math>\sqrt{2}</math>	${\sqrt {2}}$	{{math|{{radical|2}}}}	√2
<math>\sqrt{1-e^2}</math>	${\sqrt {1-e^{2}}}$	{{math|{{radical|1 &minus; ''e''&sup2;}}}}	√1 − e²

The codes on the left produce the symbols on the right, but the latter can also be put directly in the wikitext, except for ‘=’.

Syntax	Rendering
α β γ δ ε ζ η θ ι κ λ μ ν ξ ο π ρ σ ς τ υ φ χ ψ ω Γ Δ Θ Λ Ξ Π Σ Φ Ψ Ω	α β γ δ ε ζ η θ ι κ λ μ ν ξ ο π ρ σ ς τ υ φ χ ψ ω Γ Δ Θ Λ Ξ Π Σ Φ Ψ Ω
∫ ∑ ∏ √ − ± &infty; ≈ ∝ {{=}} ≡ ≠ ≤ ≥ × · ÷ ∂ ′ ″ ∇ ‰ ° ∴ Ø ø ∈ ∉ ∩ ∪ ⊂ ⊃ ⊆ ⊇ ¬ ∧ ∨ ∃ ∀ ⇒ ⇔ → ↔ ↑ ℵ - – —	∫ ∑ ∏ √ − ± ∞ ≈ ∝ = ≡ ≠ ≤ ≥ × · ÷ ∂ ′ ″ ∇ ‰ ° ∴ Ø ø ∈ ∉ ∩ ∪ ⊂ ⊃ ⊆ ⊇ ¬ ∧ ∨ ∃ ∀ ⇒ ⇔ → ↔ ↑ ℵ - – —

Image Annoation

<div class="wpImageAnnotatorEnable">
<span class="wpImageAnnotatorPageName" style="display:none;">[[Sandbox]]</span>
<span class="wpImageAnnotatorFullName" style="display:none;">[[Sandbox]]</span>
<div class="wpImageAnnotatorFile">[[File:Foo.png]]</div>
<div style="display:none;"><div><div><!--IMAGE NOTES BELOW -->{{ImageNoteEnd|id=-1}}
</div>

References and Citations

Using Native Ref Tags

In-text references make it easy to copy the text to another page; on the other hand, they make it hard to read. References containing a lot of data, quotes or elaborate citation templates can make up a significantly larger fraction of the source than the text that will actually be visible. To avoid this, recent versions of the extension allow moving some or all of the references into the <references /> section, to the place where they will actually appear to the reader. Thus,

According to scientists, the Sun is pretty big.<ref name="miller" />
The Moon, however, is not so big.<ref name="smith" />

==Notes==
<references>
<ref name="miller">E. Miller, The Sun, (New York: Academic Press, 2005), 23-5.</ref>
<ref name="smith">R. Smith, "Size of the Moon", Scientific American, 46 (April 1978): 44-6.</ref>
</references>

will have the same output as the first example above, although the numbering and order of the references will not in general be the same.

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HTML

Example

<html> <iframe src="http://www.w3schools.com/tags/tag_iframe.asp" height="100" width="400" frameborder="1" seamless="seamless" style="float:left"></iframe> </html>

iFrame Code

<html>
<iframe src="http://www.w3schools.com/tags/tag_iframe.asp" 
height="300" width="350" frameborder="1" seamless="seamless" style="float:left">
</iframe>
</html>

iFrame Attributes

Attribute	Value	Description
align	left, right, top, middle, bottom	Specifies the alignment of an iframe according to surrounding elements
frameborder	1, 0	Specifies whether or not to display a border around an iframe
height	pixels	Specifies the height of an iframe
longdesc	URL	Specifies a page that contains a long description of the content of an iframe
marginheight	pixels	Specifies the top and bottom margins of the content of an iframe
marginwidth	pixels	Specifies the left and right margins of the content of an iframe
name	name	Specifies the name of an iframe
sandbox	"", allow-forms, allow-same-origin, allow-scripts, allow-top-navigation	Enables a set of extra restrictions for the content in the iframe
scrolling	yes, no, auto	Specifies whether or not to display scrollbars in an iframe
seamless	seamless	Specifies that the iframe should look like it is a part of the containing document
src	URL	Specifies the address of the document to embed in the iframe
srcdoc	HTML_code	Specifies the HTML content of the page to show in the iframe
width	pixels	Specifies the width of an iframe

Tables

wikitable

Link	Description
BioNetGen	A web-based tool for automatically generating a biochemical reaction networks from user-specified rules for biomolecular interactions.
B10NUMB3R5	(BIONUMBERS) A database of useful biological numbers.
BioInformatics Services	BioInformatics Services is a biotechnology consulting firm specializing in using computational biology to solve complex biological and data analysis problems.
cellmigrationgateway	modeling software
CellML	The CellML language is an open standard based on the XML markup language at the University of Auckland and affiliated research groups.
CompCell Bio Web	Development site for teaching modules on quantitative cell biology.
DOQCS	Quantitative Cellular Signaling (DOQCS) is a repository of models of signaling pathways.
E-Cell	A Multi-Algorithm, Multi-Timescale Simulation Software Environment.
Gfit	A program for global regression analysis of experimental data.
Kitware	Professional Visualization Solutions, Tools and Support.
MCell	General Monte Carlo Simulator of Cellular Microphysiology.
Minimotif Miner	Application to search for short sequence motifs in Proteins.

Upgrading MediaWiki

Step 1 - download latest stable version of MediaWiki

Step 2 - determine database credentials from dreamhost

Get Hostname (e.g.)

• mysql.bradleymonk.com

Get Database name (e.g.)

• bradleymonk_com

Get Database User name (e.g.)

• username

Get Database User pass (e.g.)

• password

Step 3 - back-up existing files and the database

• Go to: mysql.example.com
• Enter db user and password when prompted
• click on db in left panel
• click on the "Export" tab
• check "Save as file"
• click "Go"

Step 4 - FTP the mediawiki.tar.gz file to the /w directory

Step 5 - Unpack the tarball

Use the console to SSH into the /w directory and unpack tarball

• $ssh bradleymonk.com -l username
• Change to the /w directory

• $tar xvzf mediawiki.tar.gz

• this unpacks into a new folder: /w/mediawiki

Step 6 - Move files and rename directory

Copy files from old to new directory

• LocalSettings.php
• logofile.png
• images (or upload) directory
• extension directory
• custom skins
• .htaccess file

Swap-rename directories

• rename old directory /w_old
• move new directory out of /w_old to top level domain
• rename new directory to /w

Step 7 - Run MediaWiki update script

• login with SSH again:

• $ssh bradleymonk.com -l username

• change to the /w/maintenance directory
• enter: $php update.php

• If the prompt gives an error like: "you're using php version 2.x mediawiki requires version 3.x"
• try entering these:

• $/usr/local/php53/bin/php update.php
• $/usr/local/php54/bin/php update.php

Check if the upgrade worked by going to the MediaWiki page "Special Version"

Quoting

“

SAN DIEGO -- Money -- does it draw students to their future careers? The answer is no, according to statistics and students at San Diego State University.

”

{{cquote|quote goes here}}

MediaWiki Tips

• To remove the arrow icon from external links, navigate to MediaWiki:Common.css and add this line of code

#content a[href ^="http://"].external {background: center right no-repeat; padding-right: 1px;}

Button Template

{{Button|TPB=.5em| Button Text }}

Button Text

Table Map

See here: Table Map

Labeled Section Transclusion

See: Extension:Labeled_Section_Transclusion

Step 1: Mark off sections

Mark off sections in the text using <section></> tags like this:

   
    <section begin=Hayashi_Malinow_2000_Science />

    {{Article|Hayashi Malinow|2000|Science • PDF|10731148|Driving AMPA receptors into synapses}}

    <section end=Hayashi_Malinow_2000_Science />
    

Note that this uses two individual markers, rather than normal XML open/close tags, which simplifies nested or overlapping sections. This allows you to insert section tags without worrying about interfering with other sections.

Step 2: Transclude the section

Call the parser function to transclude it, i.e. to transclude a section called chapter1 from a page called Articles:

   
    {{#section:Articles|Hayashi_Malinow_2000_Science}}
    

Selected & New Pages

• Category:Neuroscience Methods
• Category:Pharmacology
• Python Pubmed
• ReDiClus
• Malinow
• Molecular Methods
• Western Blot Protocol
• Qual
• Neuron Types
• Quantum Dots
• LTP
• Hippocampus
• AMPAR Tracking
• User:Monakhos
• Special:NewFiles
• Special:NewPages
• Neuroscience Tools
• Websites