Scholarpedia:Instructions for authors

From Scholarpedia

To just dive in, go to the Quick Start section and check out the visual help page.

For WikiText technical support, please contact Leo Trottier or Tobias Denninger at help@scholarpedia.org, one of whom will assign an appropriate assistant editor (student volunteer).

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" or "position" papers, but is meant to serve instead as "living reviews" that will be maintained by future generations of experts via a process of curatorship.

• "Brevity is the soulf 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.
• Scholarpedia articles do not have an abstract, introduction, conclusion, or discussion (a short "dictionary-like" definition of the main topic serves as an abstract; see below).
• Scholarpedia articles do not contain "I", "we", "our", or other first- and second-person pronouns. Encyclopedic 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
• Each article progresses from the simple to the complex.
• Whenever possible, each article starts with a one-sentence or one-paragraph dictionary-like definition of the main topic. 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, or a summary, written as accessibly but precisely as possible. While the first paragraph of the article should be quite accessible, the entire article should be written in a way accessible to advanced undergraduate students in the article's area or graduate students in adjacent areas
• The article will be most useful if the author has anticipated the most important questions associated with the topic (e.g., for a movie, this might be its director, stars, main plot, and critical response). Wikipedia articles are generally very successful in this regard.
• The article should be concise but not terse, making good use of bullet points, tables, and diagrams when these would reduce text length
• An encyclopedic article explains only the terms used in the article that are pertinent to the topic, and links 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.
• Avoid using abbreviations by spelling out abbreviations. This increases the Google PageRank of your article
• Keep references to a minimum, citing only major books and review articles. At the end of the article include "Suggested Reading" list pointing to recent or especially relevant books

Contents 1 Quick start 2 Common tasks 3 Preparation, submission, peer review, and acceptance 3.1 Submission (uploading) to Scholarpedia 3.1.1 Privacy option 3.2 Submission to Peer-Review forum 3.3 Anonymous peer review process 3.4 Acceptance 3.5 Authorship 3.6 Copyright 3.7 Curatorship 4 Password, Affiliation, and other Personal Information 5 Wikitext reference 5.1 Sections and subsections 5.2 Bullet points 5.3 Bold and Italic 5.4 Subscripts and superscripts 5.5 Tables 5.6 Including math 5.7 Including figures 5.8 Including movies 5.9 Including mp3 files 5.10 Including Java applets 5.11 Use of Copyrighted Material 5.12 Making links to other articles 5.13 Subpages

Quick start

1. Select and copy the wikitext located here
2. Navigate to your article
3. Click on the "edit this article" tab above the article's title
4. Paste in the text copied in (1)
5. Press "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 you're done with your first edits, press "Save page"

Common tasks

• Create and reserve an article: see Registration Instructions

• Change the spelling of your name, affiliation, email, or password: press 'preferences' link at the top-right corner. This is only available after signing in to Scholarpedia

• Article submission:

1. Log in,
2. Go to article,
3. Press 'edit this article' button,
4. Copy and paste article text into the main window
5. Press the 'save page' button.

• Access personal authored articles listing:, click your user name name at the top-right corner of Scholarpedia page, then press the article's title. This is only available after signing in to Scholarpedia

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

• Limited conversion from LaTeX to WikiText is possible using the conversion tool

Preparation, submission, peer review, and acceptance

Scholarpedia is well-suited to collaborative writing, since it supports near-simultaneous article authorship by multiple parties

Submission (uploading) to Scholarpedia

It is easiest to write articles using a text editor (e.g., Notepad, Wordpad, VIM, Emacs) locally computer. Once the article has been written, save it locally, and follow the Article submission instructions immediately above or in the Quick Start section

Privacy option

Authors can enable ‘privacy’ option, which would exclude everybody except the authors and the editor-in-chief from viewing and editing the article. The option can be exercised only once per article and only for 30 days.

Submission to Peer-Review forum

When the article is ready for peer-review, submit it to the anonymous peer review forum by clicking the ‘author’ tab an then clicking on the ‘submit’ button.

Reviewers are invited 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, such as MediaWiki powering this site, the peer review process of Scholarpedia 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 writes something like "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 puts 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. Indeed, instead of getting 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 all he has to do is either accept it, reject it, or further revise it.

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

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

To see reviewer comments and changes, press 'revisions' button, select two revisions, then press 'compare selected versions' button. When you address the reviewers concerns, press 'author' button, then 'email alert' button to send the reviewers an automated message that new revision is ready.

Acceptance

It is possible, and even expected, that there are many rounds of reviews, each logged as a ‘revision’, and each accessible to others to view. (For some, reading the review history may be more exciting that reading the article itself). Ideally, the article converges to the form that is acceptable to both the author and the reviewers. At this point, reviewers press the ‘Accept’ button, and the article is labeled 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 they can hold it (i.e., not accept it) for a long 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 to rename your article.

Authorship

After reviewers accept the article, the author has a chance to make the final revision 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. The article is given a page number, which should be used to cite it.

Copyright

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

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 of the article, accepting those that are valid and useful, and rejecting those that are not. You may resign from curatorship at any time you want. However, it is probably a good idea to keep your curatorship until your article is printed.

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

Password, Affiliation, and other Personal Information

To change your password, email, affiliation, or other personal information, click the 'preferences' link at the top right corner (next to your username).

Wikitext reference

Articles in Scholarpedia have 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 (do not press ‘save’ button, unless you made useful revisions to the article).

Take a look at Scholarpedia:Article Template. Just press 'view source' button, copy and paste the source into your article, then change the text to whatever you need, add more tags (sections, bullet points, etc.) as explained below.

Also, you can find a simple-minded LaTeX to WikiText converter at http://www.scholarpedia.org/wiki/tex2wiki.php. It uses context-replacement to change LaTeX math environments to <math>...</math> brackets; see also Including math below.

Sections and subsections

To create a section, write its title on a new line and surround it by two ‘==’ signs, e.g.,

== Wikitext format ==

produces the title of this section. Mark subsections as

=== Sections and subsections ===

which produces the title of this subsection. The table of content will be generated automatically for articles having three or more sections.

Use "Sentence-style capitalization" for sections and subsections.

Separate paragraphs within each section by an empty line.

Bullet points

To create a list of bullet points, start each new point with the star sign ‘*’. For example, the wikitext

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

generates

• item 1
• item 2
  • subitem 2a
  • subitem 2b
• item 3

Bold and Italic

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

Use bold for definitions and italic 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 gives your article higher Google PageRank and brings it at the top of Google (and other) search.

Subscripts and superscripts

• To make a subscript, use the  brackets. For example, I_Ca appears as I_Ca.
• To make a 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 have wikitext->latex->pdf converter, so having all equations in latex would result in more consistent texts.

Tables

Please, read Wikipedia help to learn how to include tables into wikitext.

Including math

To include math formulae, just write your LaTeX expression and surround it by <math> </math> brackets. For example,

:<math>

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

</math>

results in

Put ":" before the first <math> delimiter to tell Scholarpedia to indent (put some space before) the equation. Writing

:<math mylabel>

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

</math>

results in a number at the right-hand side

(1)

To refer to equation (1), write "equation (<ref>mylabel</ref>)".

Not all LaTeX commands are supported; see page 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 dirty copy), open your article for editing, copy and paste your text, and then press 'preview' button. Save your text only after you removed the extra LaTeX commands.

Including figures

• Step 1. To include the figure into the article, put 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 that consists of your article title and other text (to avoid overwriting somebody else's figure).
• Accepted formats include gif, jpg, and png, with size 100K or less (the figure below is only 12K).
• Step 2. When you save your text, you will see a red link in the text (where you put your placeholder [[Image:...) prompting you to upload the figure file. Just click the link and follow the instructions.
• Figures in Scholarpedia are numbered automatically; if you need to refer to them, you need to 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]]
 

It 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.1 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 a permission to reproduce the figure from that journal. (you need to do that even if you are reproducing a copyright 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 would not require readers to install any software and it would run even on cell phones and iPods. Other (less desirable) movie formats are avi, mpeg, mpg, mov. Please, keep movie files less than 1MB.

To include a movie into your article, just type

[[Media:myvideofile.avi]]

To include Flash movies, just use

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

which produces

Including mp3 files

To include an mp3 file into your article, just type

[[Media:myaudiofile.mp3]], 

which produces

If the file is not uploaded, Scholarpedia will create a red link directing you to the upload page.

Including Java applets

See detailed instructions on how to include Java applets.

Use of Copyrighted Material

Authors cannot use in Scholarpedia any works (e.g. figures already published in another location) over which there is copyright owned by some 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. This usually means, for example, including in a copyrighted figure's caption text such as "reproduced with permission".

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, and thus nobody can reproduce any part of the author's work here without the permission of Scholarpedia or the author.

A helpful exception to the above rule is that other authors of Scholarpedia 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 appropriate place (you do not reproduce the figure, you just link to the existing figure...)

An author may select 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 of what is already provided by Scholarpedia's general copyright.

Making links to other articles

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

• Internal links:
  • Surround the linking term in double square brackets. For example, [[Bursting]] links to Bursting.
  • Adding a pipe “|” and a text, e.g., [[Bursting|autonomous bursters]], results in the same link but showing the text, i.e., autonomous bursters (click on it).
  • Make internal links only when you refer to a term for the first time in a paragraph, as if you provide or remind the definition of the term.
• External links:
  • Surround an URL by one pair of brackets. For example, [http://www.sfn.org] results in [1].
  • Adding space and then a text to the link, e.g., [http://www.sfn.org Society for Neuroscience], results in a nicer 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 the autolink to attractor reconstruction, and not to attractor.
  • You can control the autolinking process using the "magic word" __AUTOLINKER{1|exclude title 1|exclude title 2} placed anywhere in the article.
  • 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. (E.g., an article on gamma ray bursts may not want to provide a link to neuronal bursting).
  • To turn off the autolinker, place __AUTOLINKER{0} anywhere in the text.
  • The default state is __AUTOLINKER{1}, i.e, only the first match for any title is converted to a link to this title.

Put section == References == at the end of the article. Keep the list of references to the 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 into the text, write [[#mylabel|Lastname et al. YEAR]] in the text and put the label <span id="mylabel"></span> next to the reference.

Put major books (not necessarily cited in the article) into ==Recommended reading==.

Finish your article with the == See also == section with links to relevant articles. Go to those articles and add appropriate links to your article.

At the end of your article, include the following links to place your article in the appropriate category, e.g.,

[[Category: Computational Neuroscience]]

[[Category: Dynamical Systems]]

You should include at least one category.

Subpages

Scholarpedia pages may have subpages. For example, this article has a subpage /First Subpage. Here, the symbol "/" at the beginning 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 complicated tree-like structure useful to create multipage courses and tutorials. To refer to a subpage from the master page, just write

[[/First Subpage]], which results in the link /First Subpage.

To refer to the subpage from other pages, write

[[Scholarpedia:Instructions for authors/First Subpage]] resulting in Scholarpedia:Instructions for authors/First Subpage.

Subpages inherit authors/curators from the master page.

Only authors/curators can create subpages, and only to their own articles. To create a new subpage, write the link to the subpage in the master page and follow it (it appears in red while the subpage is not created, and then it becomes blue). The text that appears on the subpage (prompting for listing curators) is a generic text that always appears on every new page, it can be removed.