Mr. Ben Topkins

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    Alumnus, Department of Cognitive Science, UCSD, San Diego, CA, USA

    Welcome!

    Scholarpedia is not a peer-reviewed journal, but 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 scholars are witty -- an effective Scholarpedia article is 2-3 pages long (2,000 words, though some topics warrant longer articles), not counting figures and animations.

    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 <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 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 encyclopedic entries, Scholarpedia articles are to be written in the "classic style" (Thomas & Turner, 1994, Princeton University Press). This is especially important as in 20 years article authorship will no doubt have changed.

    • Articles here should be neutral, mentioning any and all widely accepted alternate points.
    • 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 accessible to advanced undergraduate students studying in the article’s area or graduate students studying adjacent topics.
    • Authors should attempt to anticipate common questions a reader might ask about a topic (e.g., for a movie: Who directed, or starred in the film? What was the main plot? And, what critical response did it receive?). Wikipedia articles are generally very successful in this regard.
    • Articles explain only the terms that are pertinent to the topic, and link to articles where other terms are defined (see below). 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.
    • Scholarpedia articles do not contain "I", "we", "our", or other first‐ and second-person pronouns.
    • Avoid using abbreviations. This increases the Google PageRank score of the article.

    Article publication process

    Article submission

    It is easiest to develop and write articles in a text editor (e.g., Notepad, Wordpad, VIM, Emacs) on your local machine. When the article is ready for submission, save it locally, and follow the steps below, or in the Quick start section to submit the article to Scholarpedia.

    1. Log in to Scholarpedia.
    2. Navigate to the article.
    3. Click the edit this article tab above the article’s title.
    4. Copy and paste the text of the article into the main window.
    5. Click save page.

    Quick start

    Scholarpedia provides a template for authors who would prefer not to start with a blank page. Follow the steps below to apply the Scholarpedia template to your article.

    1. Select and copy the WikiText located here.
    2. Navigate to your article.
    3. Click the edit this article tab above the article's title.
    4. Paste in the text copied in step (1).
    5. Click preview to see the article template as rendered by Scholarpedia -- you can continue to edit your article using the text field at the bottom of the Preview page.
    6. When finished with your edits, click save page.

    Privacy option

    Scholarpedia offers authors the option to lock their article for editing and viewing for a 30-day period (this option can only be exercised once per article). During this period, editing and viewing of that article is restricted to the author(s) of that piece and the editor-in-chief. To activate the privacy option… how do they do it?

    Peer review forum

    When an article is ready for peer review, submit it to the anonymous peer review forum by selecting the author tab and then clicking submit.

    Reviewers are recruited by the article's editor. They are asked to follow the instructions for reviewers.

    Anonymous peer review process

    Because of the wiki-style collaborative software powering the site, the Scholarpedia peer review process is more efficient than that of printed journals.

    The reviewer’s job is simplified. If a reviewer of a journal article finds an error, he or she may write, "on page 12, paragraph 3, line 4 from the top, second equation, numerator, a minus sign is missing in the exp function...", whereas in Scholarpedia, the reviewer just inserts the minus sign where it belongs. Similarly, instead of explaining why a statement is wrong and how to fix it, the reviewer just fixes it.

    The author’s job is simplified too. Instead of receiving a review of a journal article with something like, "The statement on page 14, paragraph 2, describing the properties of the function f is not clear; please rewrite it...", and then figuring out what is not clear and how to rewrite it, the curator gets the statement already rewritten by the reviewer, and simply accepts, rejects, or further revises it.

    Reviewers may revise or rewrite your article the way they feel is best for the subject or ask you to make the revisions. Anonymous reviewers can write comments to you the old-fashioned way: Incorporating suggestions and criticism into the <review> </review> brackets, which highlight the suggestions for you. You either comply with their suggestions or reply to them by writing your explanations within the same brackets.

    Reviewers can also put their comments into the reviews section of the article (see reviews link above the article's title).

    To see reviewer comments and changes, click revisions, select two revisions, then click the compare selected versions button. After replying to the reviewers’ concerns, click the author button, then select email alert to send the reviewers an automated message that a revision is ready for review.

    Acceptance

    An article may be subject to multiple rounds of reviews. Each review is logged as a ‘revision’, and is available for others to view. (For some, reading the review history may be more exciting than reading the article itself). Ideally, the article converges to a form that is acceptable to both the author and the reviewers. At this point, reviewers may click the Accept button, labeling the article as ‘peer-reviewed’.

    The job of the reviewers is to make sure your article is correct, unbiased, and fits the description of a "good encyclopedic article". They cannot reject your article, but can hold it (i.e., not accept it) for an extended period of time; during this period, your article will show the tag "...not accepted yet; may contain inaccuracies...". If the scope of your article is too narrow, reviewers may also recommend renaming your article.

    Final revisions

    After reviewers accept the article, the author has a chance to make final revisions and then approve the article “in the final form”. At this moment, the article is labeled as ‘approved’, its final form and the author list are stored permanently in the Scholarpedia archive. And, the article is given a page number, which can be used to cite it.

    Copyright policy

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

    1. author owns the copyright and licenses the content to Scholarpedia,
    2. Creative Commons
    3. GNU FDL.

    Curatorship

    As an author of an article, you will automatically become its curator upon the article’s approval. The responsibility of the curator is to evaluate all revisions to the article, accepting those that are valid and useful, and rejecting those that are not. You may resign your curatorship at any time. However, it is a good idea to keep your curatorship until your article is printed.

    You may want to retain your curatorship after the encyclopedia is printed if you are interested in what people think about the article or what people want to add, remove, or rewrite. Remember, the philosophy of Scholarpedia is that articles outlive their authors. Imagine what your article could look like 30 years from now.

    Common tasks

    • For instructions on how to create and reserve an article, see Registration instructions.
    • Use the preferences page to change the spelling of your name, affiliation, email, or password. Click preferences in the top-right corner of the page (next to your user name) to navigate to the preferences page. (Note: preferences is only available after signing in to Scholarpedia.)
    • To access your personal authored articles listing:
    1. Log in to Scholarpedia.
    2. Click your user name in the top-right corner of the page.
    3. Select the title of the article you wish to access.
      (Note: Your user name only appears after signing in to Scholarpedia.)

    More information is available at Help, Author FAQ and on the, more detailed, Instructions for authors (Physics) page.

    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; 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

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

    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 <math> </math> tags. For example,

    :<math>

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

    </math>

    results in

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

    Add a colon (:) before the first <math> delimiter to tell Scholarpedia to indent (put some space before) the equation.

    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,

    :<math mylabel>

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

    </math>

    results in a number on the right-hand side of the equation.

    <math mylabel>

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

    To refer to equation (<ref>mylabel</ref>), write "equation (<ref>mylabel</ref>)".

    Note: Not all LaTeX commands are supported; see Help:Math for examples. A simple-minded LaTeX to WikiText converter can replace all your LaTeX math environments with <math>...</math> brackets. 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|F1|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, places a brief caption beneath it, and assigns label "F1" to the figure. The remainder of the text flows nicely around the frame. See Wikipedia picture tutorial for more information. To cite/refer to Fig.<ref>F1</ref> in the text, write Fig.<ref>F1</ref>.

    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 1MB.

    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, 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. A list of accepted categories can be found... where?

    Subpages

    Scholarpedia pages may have subpages. For example, this article has a subpage /First Subpage. Here, the forward slash (/) before the title tells Scholarpedia that First Subpage is not a separate article, but a part of the current (master) page. Subpages may have subsubpages, and so on, resulting in a tree-like structure useful for creating multipage courses and tutorials. To refer to a subpage from the master page, type, [[/First Subpage]], which results in the link: /First Subpage.

    To refer to the subpage from other pages, type, [[Help:Authors/First Subpage]] resulting in Help:Authors/First Subpage.

    Subpages inherit authors/curators from the master page.

    Only authors/curators can create subpages, and can only add them to their own articles. To create a new subpage, include a link to the subpage in the master page and click on it (the link appears in red before the subpage is created, and then becomes blue). Note: Generic text initially appears on the subpage, this text is identical on every new page, and can be removed.

    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.

    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.

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