Help:Authors

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    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.

    Contents

    Article Style

    Article Structure

    "Brevity is the soul of wit", and there is little doubt that the world's leading scientists and 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 broad 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 <strong> ... </strong> 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 more basic to more advance concepts
    • Articles should be concise but not terse, making good use of bullet points, tables, and diagrams
    • 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 broadly accessible, 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 created as a subpage of your user page. It will be there until it is sponsored by an existing Curator of Scholarpedia. You are then free to begin composing your article and inviting co-authors.

    Adding a co-author

    To add co-authors, on your article page click on the "Invite a co-author" button (top left) and follow the instructions provided there.

    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 Scholarpedia Curator who is willing to publicly attest 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 main Scholarpedia namespace. If there exists another article already sponsored but not approved yet with the same title, then your article will be placed in a queue of articles waiting to take the place of the one currently in development, should this latter one be rejected.

    Important: Once your article is sponsored, the deadline for getting the article written, reviewed, and approved is two months from the date when the article achieved "Sponsored" status.

    Peer-review

    When an article is ready for peer-review, press 'invite reviewer' on the dashboard. The article needs to be accepted by two existing Curators (an article Sponsor can also choose to serve as one of the article's reviewers).

    In general, it is the responsibility of the team of article authors to find reviewers for their article and to persuade these reviewers to approve the article for publication before the two-month deadline. If the article deadline lapses, it returns to the "proposed" (unsponsored) state and the process of sponsorship and review needs to be restarted.

    You may wish to direct the reviewers you invite to instructions for reviewers.

    Publication

    After the article has been formally approved by two qualified reviewers it moves to "in-press" status. During this cool-down period, editors of Scholarpedia have an opportunity to make sure that this article did not reach "published" status erroneously. After this period ends, any of the authors can choose to approve the very first "official" version of the article for publication -- when doing so, the person who approves the article must select from among the article co-authors the individual who is the most established expert on the article's topic, as it is this individual who will become the article's Curator. The moment of final author approval is time of official archival publication.

    Copyright policy

    In brief, authors retain copyright over their works, and grant to the general public limited rights to reuse their work under a Creative Commons Attribution-NonCommercial-ShareAlike license, and grant to Scholarpedia additional rights beyond the Creative Commons license. Note that these terms only come into effect for articles once the article is published -- the public has no rights to the use of articles that are "in progress". Please see the Scholarpedia:Terms of Use for more information.

    Wikitext formatting

    Articles in Scholarpedia are in Wikitext format, a markup language designed to be much simpler than LaTeX or HTML. Wikipedia's help pages provide comprehensive information on how Wikitext works, but often it is enough to look at an existing article, e.g., Bursting, and inspect the article's source text (but, do not click save, unless you made useful revisions to the article).

    Another way to get started is to take a look at Article Template. To use the template, just click edit, 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 contents 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

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

    Bold and italics

    To make a word appear in italics, 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 <strong>...</strong> 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 <sub> </sub> brackets. For example, I<sub>Ca</sub> appears as ICa.

    To make text appear as superscript, use the <sup> </sup> brackets. For example, Ca<sup>2+</sup> 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.

    It is often helpful to 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|title to exclude 1|title to exclude 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>
    

    both 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. Keep in mind that if you later want to create an internal reference to the figure/image you must not include any spaces in the filename (so "Bursting Examples.gif" becomes "Bursting_Examples.gif").

    Accepted file formats include gif, jpg, and png, with a file size of 2MB or less (the figure below is only 12K). To convert images, see next section.

    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.

    Step 3. 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.)


    Converting image formats

    You may need to convert your images into another format. PNG is the recommended file format for static images, although JPEG and GIFs are also accepted, among some others. Postscript and PDF files are not accepted formats for images.

    ImageMagick is helpful for converting images. You can use a command such as:

    mogrify -density 200 -flatten -format png *.ps
    

    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.

    Note: Animated .gif files are included in the same manner as normal .gif files (i.e., [[Image:Animation.gif|thumb|400px|right|F2|This figure is animated]]).

    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 <span id="mylabel"></span> next to the reference.

    You can also submit your references in BibTeX format or directly include them in your online article using Scholarpedia's Bibitem template, please see Instructions for authors (Physics) 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").

    Note that other authors of Scholarpedia articles can freely use figures from each other's 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).

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