Help:ABC extensions syntax

Extension Syntax

Several extension use special syntax. This is a synopsis.

LST

LST (Labeling a section for transclusion)

<section begin=exercises />
...
<section end=exercises />

LST (Transcluding a labeled section)

{{#lst:Transcriptome|exercises}}

Common sections are: reading and exercises.

Syntax Highlight

GeSHI

<source lang="R"> yadda <- "yadda" #yadda</source>

 yadda <- as.character("yadda") #yadda

• lang="??"
• line="GESHI_NORMAL_LINE_NUMBERS|GESHI_FANCY_LINE_NUMBERS"
• line start="??"
• highlight="??"
• enclose="pre|div|none" ... (div induces wrapping))

Pubmedparser

{{#pmid:12345678}}

This inserts the article information in a <div>, formatted by Template:Pubmed.

{{#pmid: 15289071 |Steipe2004}}

This formats the output for the Cite extension; A footnote mark will be inserted at the edit location and the actual reference will appear beneath the <references /> section of the page.

Non-Pubmed pdf

If the article is not on PubMed, upload it to the repository, enter bibliographic details and make sure file the filename is unique with full extension.

{{PDF
|authors= 
|year= 
|title= 
|journal= 
|volume= 
|pages= 
|URL= 
|doi= 
|file= 
|abstract= 
}}

Ambrish, R. & Zhang, Y. (2012) Protein Structure Prediction. Encyclopedia of Life Sciences

(pmid: None) [ Source URL ] The goal of protein structure prediction is to estimate the spatial position of every atom of protein molecules from the amino acid sequence by computational methods. Depending on the availability of homologous templates in the PDB library, structure prediction approaches are categorised into template-based modelling (TBM) and free modelling (FM). While TBM is by far the only reliable method for high-resolution structure prediction, challenges in the field include constructing the correct folds without using template structures and refining the template models closer to the native state when templates are available. Nevertheless, the usefulness of various levels of protein structure predictions have been convincingly demonstrated in biological and medical applications.

Cite

Inserting a footnote

<ref>A note in ref tags will insert a footnote mark,
 linked to the text in the <references /> section of the page.</ref>

This is the text.

---

Misc.

Math markup

<math>H = - \sum_{i=0}^n p_i \log_{2} p_i</math>

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle H = - \sum_{i=0}^n p_i \log_{2} p_i}

see: http://meta.wikimedia.org/wiki/Help:Formula

Inserting a Web-site box

{{WWW|WWW_UniProt}} 

UniProt [ link ] [ page ] UniProt is the protein sequence database of the European Bioinformatics Institute. It is an extraordinarily well constructed, curated, and integrated resource. As a public resource, its results are freely accessible world-wide. The "Knowledge Base" (UniProtKB), which is the database proper, contains two subsections: SwissProt, the manually curated and heavily annotated protein sequence repository; it is approximately equivalent to the NCBI Refseq protein database, albeit with usually higher annotation levels. TrEMBL is much larger and contains sequences that have been computationally translated from the EMBL nucleotide sequence collection. It is approximately equivalent to the NCBI's Entrez protein database. The URL links to the entry for the Saccharomyces cerevisiae cell-cycle regulation transcription factor Mbp1.

Inserting a Web-link box

<div class="reference-box">[http://www.ncbi.nlm.nih.gov '''The NCBI''']</div>

The NCBI

Linking text to R documentation

{{R|plot}} and {{R|exists|base}} and {{R|colorRamp|grDevices|colorRampPalette}}

plot and base and colorRampPalette

The graphics package is default, other packages can be chosen with the template's second parameter. Check at the ETH for which package directory to choose. If a third parameter is present, that will be the linked text.

Linking text to Wikipedia

{{WP|Mutual information|Mutual Information}}

Mutual Information

Collapsible elements

See: Manual: Collapsible elements

 <div class="mw-collapsible mw-collapsed" data-expandtext="Expand for poem" data-collapsetext="Collapse" style="width:40%; border:solid 1px; background-color:#F6FFE6; padding:10px;">
 '''The Road Not Taken'''    <small>''Robert Frost''</small>  
 <div class="mw-collapsible-content">
 Two roads diverged in a yellow wood,<br />And sorry I could not travel both<br />
     [...]
 I took the one less traveled by,<br />And that has made all the difference. 
 </div>
 </div>

The Road Not Taken    Robert Frost

Two roads diverged in a yellow wood,
And sorry I could not travel both
And be one traveler, long I stood
And looked down one as far as I could
To where it bent in the undergrowth;
 
Then took the other, as just as fair,
And having perhaps the better claim
Because it was grassy and wanted wear,
Though as for that the passing there
Had worn them really about the same,
 
And both that morning equally lay
In leaves no step had trodden black.
Oh, I marked the first for another day!
Yet knowing how way leads on to way
I doubted if I should ever come back.
 
I shall be telling this with a sigh
Somewhere ages and ages hence:
Two roads diverged in a wood, and I,
I took the one less traveled by,
And that has made all the difference.