Proper referencing

Citing with the Cite Extension

The Cite extension is a handy and intuitive extension that lets you cite with superscripts and create a reference list at the bottom of a page. The official usage page has very easy to follow instructions on how to cite correctly in an article, and some of the methods will be recapped here. The extension uses an HTML tag, ref to create the reference

Citing with the Template and CiteULike

Because we want to be able to annotate our citations, we have a group running on CiteULike that houses most (if not all the papers) that are cited here. Although doing compound citations is not hard, its time consuming so there is written template to make it easier to do both the main citation, and the CiteULike reference. It has very simple syntax and is

{{Cite| uniqueID | Main citation text | URL to the CiteULike link (optional)}}

This is equivalent of using a citing multiple times entry. This template does mandate the uniqueID which is good practice anyways.

There are two ways to implement this template and a full example will be shown below:

• Optimal: Use uniqueID's in text and build references at the end.
  1. Every time you wish to cite, invoke the Cite template and only supply the uniqueID, e.g. {{Cite| Doe2013}}
  2. Create a <references> </references> block at the end of the document
  3. Inside the references tags, invoke the full Cite template filling in all the fields

     Note: You will need the full citation before any of the shorthand citations work.

• Alternate: Provide full citation on first use and use alternate references section
  1. The first time you use a uniqueID, use the full version of the Cite template
  2. All subsequent citations of the uniqueID can use the shorthand, {{Cite| Doe2013}}
  3. Use a <references /> at the bottom of your page

Since the first method is preferred, only an example of it will be shown.

Example Citation

If you provide a page that looks like:

 Hydrogen is an element {{Cite| Doe2013}}. 
 I will not cover it here, but there are numerous reviews of alchemical simulations at Alchemisty.org.{{Cite| MyUniqueID}}{{Cite| ASecondID}}. 
 Did I mention Hydrogen?{{Cite| Doe2013}}

 <references>
 {{Cite | Doe2013 | John Doe is a made up person| http://www.citeulike.org/}}
 {{Cite | MyUniqueID | By having the full citation here...}}
 {{Cite | ASecondID| ... It avoids clutter in the main text.}}
 </references>
 

You will get the following:

Hydrogen is an element . I will not cover it here, but there are numerous reviews of alchemical simulations at Alchemisty.org.. Did I mention Hydrogen?

Simple Citation

Simply enclose the citation text in the HTML tag

<ref>A Citation!</ref>

to give the following result

Citing Multiple Times

If you need to use a refference multiple times on the same page, simply pass the argument "name" to the HTML tag like so:

<ref name=uniqueID>A Citation with an identity tag!</ref>

replacing the word "uniqueID" with whatever identifier you want. This will make it so that when you need to use the reference again, you can just use the shortcut method:

<ref name=uniqueID />

Note that there is no closing tag and the backslash is important. If you were to create another reference with the same ID, only the first complete instance of a reference with that ID is parsed; all subsequent references with that ID are treated like the first instance and the text between them is ignored. To better illustrate this, consider this example:

<ref name=test>The citation that will show up!</ref>
<ref name=test>This text will not show up at all, write to your heart's content, so long as you close the tag</ref>

yields... the same citation!

Legacy Method

The sections below are how citations should be done without the Cite extension installed. Since Sept 2012, the Cite extension makes it so we can cite in a style similar to Wikipedia. To do this, please see the section above.

Selecting a unique name

To add a reference, first select a name. To name the paper uniquely, name it {FirstAuthorName}{JournalAbbreviation}{Year}{letter} where the 'letter' is a,b,c, and so forth, noting duplicates.

So M. R. Shirts and V. S. Pande, J. Chem. Phys. from 2005 becomes MRShirtsJChemPhys2005a.

Papers that have not yet appeared in print editions are fine, as long as you can provide a link to an online version of the article through the journal site. If you wish to link a preprint, add "Preprint" after the journal name (or in place of the Journal name if there not yet a journal), and replace it when it has been published.

If you are not sure of the journal abbreviation, please look it up [here]

Adding the reference

In MediaWiki, one must first add the name to existing text, and then save it (i.e., it cannot be created free floating). It most cases, papers will be added because they are being added as references in already created text. If you just want to add it, save the name to -any- page, add the reference, categorize it, and then delete the reference in the page that linked to it. Be sure to at least categorize it, or else it will be lost!

If you wish to add a citation, but want the link to appear with alternate text, that can be done by

    [[name | alternate text here]] 

Following these practices will make it easier to modify this database later!

Information in the reference

Reference creation is very easy. Simply start with:

{{Reference}}

to access the Reference template. From there, add variables to add information in the format:

{{Reference|title=your title|first author=your first author}

And so forth. For example:

{{Reference|
 first author = Jayachandran|
 authors = Guha Jayachandran, Michael R. Shirts, Sanghyun Park and Vijay S. Pande| 
 group = Pande Group | 
 year = 2006 | 
 volume = 125 | 
 pages = 084901 | 
 doi = 10.1063/1.2221680 |
 title = Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics|
 journal = J. Chem. Phys.}} 

This will automatically produce a properly formatted reference, along with automatically categorizing it by year, by first author, and by group, and provide a link to the DOI. The order does not matter, as long as the variable names are correct.

Any commentary you can add is also very important! Let us know what other papers it depends on, and what other papers it has influenced.

Adding categories

At the end, add categories to which the reference belongs, in addition to the automatically generated categories. All papers at least belong to the category of the year of their paper. Categories are added by the text:

    [[Category:Solvation Free Energy Calculations]]

Courtesy

Please be polite when editing the commentary on references! Don't discredit research unless you have solid reasoning, or a link to a study that contradicts it.