User:Jonathan R. Williford/Help:Authors

Welcome!

Scholarpedia is a peer-reviewed encyclopedia written by the leading experts of their respective fields. As an encyclopedia, it does not publish research papers or position papers, but, instead, is meant to serve as a repository for "living reviews" to be maintained by future generations of experts via a process of curatorship.

Article Style

Article Structure

"Brevity is the soul of wit", and there is little doubt that the world's leading scholars are witty -- an effective Scholarpedia article is 2-4 pages long (2,000 - 4,000 words), not counting figure captions or references.

While Scholarpedia articles do not feature an abstract, introduction, conclusion, or discussion, there are common structural elements most articles share. Whenever possible, each article starts with a one-sentence or one-paragraph dictionary-like definition of the main topic (this line essentially serves as an article abstract). The first paragraph of an entry should be conceptually accessible to a wide audience of readers. For instance:

"A neuronal burst of spikes is two or more action potentials followed by a period of quiescence."
"A dynamical system is a system whose state in any moment of time is a function of (1) its immediately previous state and (2) any input."

(Please use ... to bracket the mention of the article's topic in its definition, as this will improve its ranking in Google search results).

Then, as applicable, each article provides examples, illustrations, and a summary. In addition, wherever possible, articles are written in accordance with the following guidelines:

Each article progresses from the simple to the complex.
Articles should be concise but not terse, making good use of bullet points, tables, and diagrams, where these implements can break up text.
The end of each article should include sections for references, recommended reading, and related Scholarpedia articles. See References below for more information.

Writing style

As entries in an encyclopedia, Scholarpedia articles are to be written in "classic style" (as described in "Clear and Simple as the Truth" by Thomas & Turner, 1994, Princeton University Press). The writing must withstand the test of time, and continue to read well in spite of a change in who is responsible for the article's content (e.g., the first-person and second person must be avoided).

Furthermore,

While Scholarpedia aims to be accessible to a wide audience, content should be sufficiently comprehensive as to be informative for those in fields relevant to the topic of a given article. As a general rule, articles should be targeted to advanced undergraduate students studying in the article’s area or graduate students in related areas.
Authors should attempt to anticipate common questions a reader might ask about a topic (e.g., for an invention: who invented it, when, where, why, and how? What did the invention replace? What was its impact? Has it led to any notable successes or failures?). Notice that, e.g., Wikipedia articles are generally very successful in this regard.
Articles here should reflect expert consensus, mentioning any and all widely accepted alternative perspectives on issues of controversy.
Articles must explain only the terms unique to the article or not appropriately explained elsewhere, and in all other cases provide links the definitions of other terms. For instance, the article on Bursting does not explain concepts such as neurons, spikes, currents, and bifurcations, but links to other articles for definitions of these terms.
Avoid using abbreviations, as it can make it more difficult for readers to find the article via Google and other search engines.

Article publication process

Article proposal

To propose an article, click 'Propose a new article' link (left menubar). Your title should be short and encyclopedic, yet descriptive. The article will be temporary placed in a subpage of your user page. It will be there until it is sponsored by an existing Curator of Scholarpedia (in the future: two Curators). You can start writing your article.

Add a co-author

To add co-authors, go to your article and click 'co-author' link on the right menubar. Copy the secret URL and email it to your co-authors. When they click on the URL, they will be able to join you as co-authors. Keep the URL confidential, as it allows people to see your email address (for verification) and to delete your proposed article. You can add co-authors at any time until the article is accepted by all reviewers.

Get Sponsorship/Validation

Your proposed article must be sponsored by an existing Curator. For this, you need to click 'sponsor' link on the right menubar. Copy the secret URL and email it to a Curator of Scholarpedia who can validate that

the topic you propose is encyclopedic and worthy a separate article, and
you are the top world expert on this topic or you are the original inventor of this topic.

Once your article is sponsored, it is moved from your user page subpage to the article (main) namespace. If there exist another article sponsored but not approved yet with the same title, then your article will be placed in the queue so that if the other article is rejected, you will take the place.

Important: Once your article is sponsored, you have 2 months to finish the writing and peer-review process.

Peer review

When an article is ready for peer review, click 'peer-review' link on the right menubar and send the secret URL to your reviewers. Your article needs to be accepted by 2 existing curators of Scholarpedia, one of whom should be the original sponsor.

It is your responsibility to find the reviewers and to get them accept your article before the two-month deadline. If you fail, your article will return to the user subpage state and you will need to restart the process of sponsorship and review.

In your email to reviewers, direct them to the page containing instructions for reviewers.

Publication

After reviewers accept the article, it will be in "in-press" status for 2 weeks so that editors of Scholarpedia can have the final veto. After that, the senior author (selected by sponsors and reviewers) becomes the Curator and he/she has to approve the very first "official" version for publication. This version will be shown to all visitors by default. The moment of approval is the publication moment for citation purposes.

Copyright policy

Each article in Scholarpedia has its own copyright policy, freely selected by the authors from the following options:

Wikitext formatting

Articles in Scholarpedia are in Wikitext format, which is much simpler than LaTeX or HTML. Refer to Wikipedia help to learn the tricks and capabilities of Wikitext. In addition, you may open an existing article, e.g., Bursting, for editing, and take a look at the format (But, do not click save, unless you made useful revisions to the article).

Take a look at Article Template. To use the template, just click view source, then copy and paste the source content into your article. Once you have applied the template to your article, you can change the text to suit your needs (For example, add more tags for sections, bullet points, etc., as explained below).

If you would like to use LaTeX, you can find a simple-minded LaTeX to Wikitext converter here. It uses context replacement to change LaTeX math environments to <math>...</math> brackets; but see also Including math below.

Text formatting

Sections and subsections

To create a section, write the section title on a new line and surround it with two equal signs (==). The example below produces the title of this section.

== Wikitext formatting ==

For subsections, use multiple equal signs. The example below produces the title of this subsection.

=== Sections and subsections ===

The table of content will be generated automatically for articles containing three or more sections.

Use sentence-style capitalization for section and subsection titles. Separate paragraphs within each section with an empty line.

Bullet points

To create a list of bullet points, insert an asterisk (*) at the start of each line. For indented bullets insert two asterisks in front of the line, for example:

*item 1 
*item 2
**subitem 2a
**subitem 2b
*item 3

generates

item 1
item 2
- subitem 2a
- subitem 2b
item 3

Lists

To create a numbered list, insert a number sign (#) at the start of each line. For subitems insert two number signs at the start of the line, for example:

#item 1
#item 2
##subitem 1a
##subitem 1b
#item 3

generates

item 1
item 2
1. subitem 1a
2. subitem 1b
item 3

Bold and italics

To make a word appear in italic type, surround it with two single quotes (''). For example, ''hello'' appears as hello.

To make a word appear in boldface type, surround it with three single quotes ('''). For example, '''hello''' appears as hello.

Use bold for definitions and italics for emphasis. For example, "... Washington, DC is the capital of the USA. Do not confuse it with the state of Washington..."

Use ... brackets at the top of the article when you define your main topic. This improves your article’s classification in Google PageRank and its placement in Google (and other search engine) results.

Superscripts and subscripts

To make text appear as subscript, use the brackets. For example, ICa appears as I_Ca.

To make text appear as superscript, use the brackets. For example, Ca2+ appears as Ca²⁺.

Do not use HTML tags for math equations, even simple ones. In the future, Scholarpedia will feature a Wikitext->LaTeX->pdf converter, so formatting all equations in LaTeX will result in more consistent texts.

Tables

Please read Wikipedia help to learn how to produce tables in Wikitext.

Links

Links in articles can be internal, referring to other articles within Scholarpedia, or external, referring to other websites. Wikipedia help provides a detailed description of the many capabilities of links. Some basic features are explained below.

Internal links

To create an internal link, surround the linking term in double square brackets ([[]]). For example, [[Bursting]] links to Bursting.

Adding a pipe (|) and text, e.g., [[Bursting|autonomous bursters]], results in a link to the same article, but allows you to define the text of the link, i.e., autonomous bursters (click on it).

Only make internal links on the first reference to a term in a paragraph, as if to provide, or remind your readers of, the definition of the term.

External links

To create an external link, surround a URL with one pair of brackets ([]). For example, [http://www.sfn.org] results in [1].

Adding space and text to the link, e.g., [http://www.sfn.org Society for Neuroscience], results in a link to the same URL, but allows you to define the text of the link, i.e., Society for Neuroscience.

Provide relevant external links at the end of your article.

Automatic links

Unlike Wikipedia, Scholarpedia can generate automatic links to existing articles; Words and phrases in an article that correspond to titles of other articles are automatically replaced by links to those articles. Scholarpedia tries to match the longest title first. E.g., the phrase "..using attractor reconstruction method.." will result in an autolink to the article on attractor reconstruction, and not to attractor.

You can control the autolinking process by inserting the following text anywhere in the article:

__AUTOLINKER{1|exclude title 1|exclude title 2}

The first argument limits the number of autolinks to any particular title, and the other arguments, separated by the pipe "|" are the titles of the article that should be excluded from the autolinking process. For example, this may be useful in an article on gamma ray bursts, where autolinks to neuronal bursting would not be desirable.

To turn off the autolinker, place the following line anywhere in the article:

__AUTOLINKER{0}

The default state is __AUTOLINKER{1}, i.e, only the first match for any title is converted to a link to this title.

Math formulae

To include math formulae, write your LaTeX expression and surround it with the beginning and ending markers as described below.

Inline math

For inline math, you can use

\( ... \) , or
<math> ... </math>

Thus \( \frac{3}{2} < 2\lambda \), and can be inserted

\(\frac{3}{2} < 2\lambda\) , or
<math> \frac{3}{2} < 2\lambda </math>

Display math

"Display", or centered, math can be wrapped using:

\[ ... \], or
:<math> ... </math>

Thus

\[ f(x) = \lim_{T \rightarrow \infty} \frac{1}{T} \int_0^T g(x, t) \, dt \]

and

:<math>f(x) = \lim_{T \rightarrow \infty} \frac{1}{T} \int_0^T g(x, t) \, dt</math>

result in \[ f(x) = \lim_{T \rightarrow \infty} \frac{1}{T} \int_0^T g(x, t) \, dt \]

Adding a text label for your equation within the math tag, numbers the equation and makes it easier to reference in your text. For example,

\[ \label{mass_energy} e=mc^2 \]

results in a number on the left of the equation: \[ \tag{1} E=mc^2 \]

To refer to equation (1), write "equation \eqref{mass_energy} ".

Because Scholarpedia uses the insanely powerful MathJax, nearly all Plain TeX Math macros are supported. For more details, visit the MathJax \(\TeX\) documentation

For short bits of text, you can use an online LaTeX to Wikitext converter. To preview your Wikitext (without saving the draft copy), open your article for editing, copy and paste your text, and then click preview. Save your text only after removing the extra LaTeX commands.

Including figures

Step 1. To include a figure in an article, type the placeholder [[Image:filename.ext]] in the text where you want the figure to appear (Here, filename.ext is the name of your image file). Use a unique name for your image filename, consisting of the title of your article and some other text (to avoid overwriting someone else's figure).

Accepted file formats include gif, jpg, and png, with a file size of 100K or less (the figure below is only 12K).

Step 2. After you save your text, a red link appears (where you put your placeholder [[Image:...]]). Clicking the link prompts you to upload the figure file. Click the link and follow the on-screen instructions to upload your image.

Figures in Scholarpedia are numbered automatically; if you need to refer to them, you can create a label, see below.

Avoid complicated figures with sub-figures and long captions. The following format is probably the most common for figures; It is used to include the figure below.

[[Image:Bursting_Examples.gif|thumb|400px|right|This figure is less than 12K]]

Figure 1: This figure is less than 12K

The Wikitext above creates a smaller version of the image (size 400px), frames it, puts it on the right-hand side and places a brief caption beneath it. The remainder of the text flows nicely around the frame. See Wikipedia picture tutorial for more information. To cite/refer to Figure 1 in the text, write

<figref>Bursting_Examples.gif</figref>.

If you reproduce a figure from an article in a journal, it is probably protected by the copyright. You need to obtain permission to reproduce the figure from that journal. (Note: Permission is required even when reproducing a copyrighted figure on your website.)

Including movies

The best way to include a movie is to make an animated .gif file, as in Synchronization. Such an animation does not require readers to install any additional software for viewing and even runs on cell phones and iPods. Other (less desirable) supported movie formats include avi, mpeg, mpg, mov. Please keep movie files to less than 1 MB.

To include a movie file in your article, type:

[[Media:myvideofile.avi]]

To include flash movies, type:

<flash>file=PinnaIllusion3.swf|width=500|height=500|quality=best</flash>

which produces:

Including mp3 files

To include an mp3 file into your article, type:

[[Media:myaudiofile.mp3]]

which produces:

Media:myaudiofile.mp3

If the file is not already uploaded, Scholarpedia will create a red link in the text. Clicking on this link will take you through the process of uploading the file for inclusion in your article.

Including Java applets

See detailed instructions on how to include Java applets.

References

Include a section entitled “References” (== References ==) at the end of the article. Keep the list of references to a minimum, ideally less than 20. Cite only major contributions, books, or review articles that are widely available. Use Harvard referencing style: "(Lastname et al. YEAR)” within the text of an article, and full citations in alphabetical order at the end. If you want to include a link to a reference in the text, type [[#mylabel|Lastname et al. YEAR]] in the text and put the label next to the reference.

References should be written in the following format:

Albero(2001). Pizza Capricciosa. Journal of pizza eaters 27: 121-127. arXiv:0808.000
Albero, Antonio; Bocca, Bill and Cuoco, C T (2003). Pizza Quattro Stagioni. Journal of pizza eaters 34(4): 12.

There are several templates that are available to help with formatting, please see Help:References for more information.

Include major books (not necessarily cited in the article) in a section entitled “Recommended reading” (==Recommended reading==).

Finish your article with a “See also” section (==See also==) section with links to relevant Scholarpedia articles. Also, go to those articles and add appropriate links to your article.

At the end of your article, include these links to place your article in the appropriate category. For example:

[[Category: Computational Neuroscience]]

[[Category: Dynamical Systems]]

You should include at least one category.

Using copyrighted materials

Scholarpedia authors cannot use any content under a copyright owned by any party other than the author, or over which there are any other publishing restrictions, unless the author has obtained the necessary permissions from the copyright and/or license holders. This rule applies to all parts of Scholarpedia, including the author's own profile page. It is the author's responsibility to ensure that he or she abides by the terms of any licensing agreement permitting the inclusion of the copyrighted material. Often these terms stipulate, for example, that the author must include a phrase such as, "reproduced with permission" in the caption text for a copyrighted figure.

Note that in many cases there is no charge associated with obtaining permission from scholarly journals to re-publish one's own figures. Many journals have a streamlined process for issuing rights and permissions (e.g., see the Nature Publishing Group's "Permission requests").

It should be additionally noted that if an author puts his/her work on Scholarpedia, it is protected by Scholarpedia copyright. Content posted on Scholarpedia cannot be reproduced without the permission of Scholarpedia or the author (unless the author selects GNU or Creative Commons license).

A helpful exception to the above rule is that other authors of Scholarpedia articles can freely use figures from each others' pages. For example, if the author of an earlier article puts up figure XYZ.gif, then nothing stops you from writing Image:XYZ.gif in your article, which would result in the figure appearing in the designated space (this is not a reproduction of the figure, just a link to the existing figure).

An author may elect to put a tag into the caption of the figure saying, "copyrighted by ...", but this is not necessary, since it does not provide more protection above that which is already provided by Scholarpedia's general copyright.