Proteins

NOTICE: This account is retired. It served as a legitimate alternate account for WillowW, in compliance with Wikipedia's policy on such accounts. It was used mainly for outreach to scientific organizations, research on Wikipedia, and developing software tools and tutorials for Wikipedia users. Please redirect future questions, discussion, or requests to WillowW.

A series of Wikipedia tutorials

I've begun a series of "bitesize" tutorials for editing Wikipedia. In addition to the webpages below, I've also made the corresponding screencast presentation. They're still rather rough, but I hope they're helpful to newbie editors.

Finished

Half-finished

Begun

On the drawing board

Workshops for scientific societies

ASCB workshop in December 2008

The American Society for Cell Biology (ASCB) has invited Tim Vickers and me to introduce its members to editing Wikipedia, specifically cell biology articles, at its 2008 annual meeting in December 2008. Here is our welcome page for the scientists, and we've begun writing a practical tutorial for scientists here. As described in that tutorial, This article template is designed to help the scientists begin editing quickly.

Final slides of the presentation

Practical tutorial in editing Wikipedia

Practical tutorial in editing Wikipedia; click on "show" to reveal

This tutorial outlines the practical steps of writing a new Wikipedia article and developing it into a Featured article, that is, one of Wikipedia's best articles.

Please begin by getting a user account

Without a user account, you won't be able to create or move pages, which would make this a very short workshop. ;) If you haven't already, please start a user account by clicking on the blue link in the topmost right-hand corner, the one labeled Log in / create account. On the following page, click on the blue link labeled Create one. On the final page, please read the information, fill in the form, and click the button labeled Create account to start your account. On the next page, you should see that the Log in / create account link has been replaced by your user name highlighted in red, followed by some user commands such as my talk, my preferences, my watchlist, my contributions, and log out. These steps are shown in the video above.

Edit in your sandbox

If you are viewing this page for the first time, the following link User:Proteins/Tutorial_sandbox should be colored red, meaning that Wikipedia has no article under that name. Open that link in a new tab, type in a few characters, and click on the Publish page button near the bottom. Your "tutorial sandbox" page should have been created and your text should have been saved and published there. Congratulations — you're a Wikipedian! You can return to this sandbox to write drafts for articles, to try out new editing methods, or simply to experiment.

Let's add a link to another article on Wikipedia! Edit your sandbox and add the text "[[mitochondrion]]". After saving, you should see mitochondrion highlighted in blue. Clicking on that blue link will take you to the Wikipedia article by that name.

By custom, topics on Wikipedia are usually given in the singular, e.g., mitochondrion rather than mitochondria, or proteasome rather than proteasomes. Plurals and other variations on the article name can be made in two ways...

by adding letters after the closing double brackets of the link. Thus, "[[proteasome]]s" produces proteasomes.
A completely different name can be given to a link using a vertical bar within the double brackets. For example, "[[chloroplast|random cellular organelle]]" will appear as random cellular organelle.

Checking whether an article on your topic exists already

You're the world's authority on a topic and you'd like to share your expertise with the world — great! But before you create a new article on your topic, you should check whether it exists on Wikipedia already. Here are two ways to do that:

Use Wikipedia's own search box in the left column. Enter “mitochondrion” in the box and click the Go button.
Conduct a Google search restricted to Wikipedia. Enter “mitochondrion site:en.wiki.x.io” in the search box for Google.

A third, more serendipitous, technique is to identify a related article, and click on the most appropriate Category at the bottom of that article. That will take you to a list of many of Wikipedia's articles under that category. For example, Golgi apparatus is categorized under Category:Organelles; going to the latter link reveals many of Wikipedia's articles on organelles.

Regardless of the method, your search will reveal one of three possibilities:

your topic has its own article (possibly under a synonym),
your topic is covered as a subsection of another article, or
your topic isn't mentioned on Wikipedia.

In the first two cases, you can improve the article, whereas in the latter two cases, you may wish to create a new article.

You may find that an article on your topic exists on Wikipedia under one name but is missing a key synonym. For example, the “Krebs cycle” article may exist, but a “citric acid cycle” article may not. To introduce the synonym, you can create a redirect page. Click on the red link for the synonym, type the words #redirect [[article name]] and save this text by clicking "Publish changes". After that, any visitor to Wikipedia who searches for your synonym will be taken to the correct article. More details on how to create an article are given in the next section.

Redirect pages are also useful for smaller topics that might not merit their own article. You can create a redirect to a specific sub-section of a larger article using a pound sign "#". For illustration, clicking on the link Golgi apparatus#Vesicular transport takes the reader to the "Vesicular transport" section of the Golgi apparatus article.

You may also find that your chosen topic has an alternate meaning in an entirely different field, e.g., “primer”. For such cases, Wikipedia has “disambiguation” pages, which direct the reader to the relevant article. Usually, the field of a term is specified in parentheses, e.g., primer (paint), primer (gasoline engine) and primer (molecular biology).

Creating an article

Creating a new article is relatively easy on Wikipedia. Wikipedia has two types of internal links: blue links that point to another article and red links that point to nothing. Clicking on a red link and beginning to edit creates an article. You may get such a red link from the Wikipedia search in Step 1, or by editing another article to add the link, e.g., "[[new article name]]". The latter method is useful when the article has unusual characters not found on an ordinary keyboard. Many unusual characters, such as Å or μ or ±, can be found at the bottom of the editing screen, under the Publish page button; select the set of characters you wish to use from the drop-down menu and then click on the desired character to add it into the text at the cursor position.

If your topic has its own article already, you should generally work on improving that rather than creating a new article. However, if you create a redundant article inadvertently, this can be fixed by merging the two articles. Merging is best done with the help of a friendly WikiProject and an administrator.

Basic editing

Once you've opened an edit window, it's relatively easy to add text: simply type and then click on the "Publish page" button below the edit box. Before you do so, though, please add a short edit summary into the box just above the button, describing the change you made. That will help you and others to remember or identify when changes occurred.

When you reach the edge of the edit window, you don't need to hit return; just keep typing! The text will automatically format itself when you click "Publish page". To break the text into paragraphs, add exactly one blank line before starting the next paragraph. Adding two or more lines is feasible, too, but it leaves too much white space on the page.

Writing the article

Wikipedia articles have two parts: a lead section of 1-4 paragraphs and a body or main article section that follows. The lead section is an abstract of the article: technical details, caveats and the like are usually omitted; it should be comprehensible to a broad audience. The body of the article is written as a mini-review article, almost always fewer than 50 kilobytes in readable prose; for scientific or other scholarly topics, the writing is typically aimed at junior-level undergraduates.

A Wikipedia article differs from a mini-review in two key ways:

Wikipedia does not allow speculation or original syntheses of the data. Assertions must be citable to scholarly literature.
Wikipedia articles are not aimed at fellow experts, but rather at interested lay-people. Examples of such readers include high-school students who might join the field someday, college students taking their first course, adults trying to educate themselves and citizens whose taxes support scholarly research. Consequently, authors cannot assume an extensive background knowledge. To supply that background, the wiki-editor can either include it themselves, or include a wiki-link to another article that explains the topic.

For some topics, the length restriction of 50 kilobytes may seem too short, especially when writing out explanations for the non-scientific reader. However, Wikipedia wants its articles to be able to be read in one sitting. To keep the article length short, major sections may have to be spun off as sub-articles and and replaced with a 1-2 paragraph summary.

Wikipedia articles make liberal use of sections and subsections to organize the article. The section and subsection titles are automatically collected at the top of the article in a Table of Contents, giving an outline of the article. To create a section, place the section name enclosed by at least two equal signs at the beginning of a line, e.g., "==History==". Subsections are created by adding an equal sign on either side, e.g., "===Medieval conceptions===". At the lowest level, sections typically have a few paragraphs and typically one image.

You will likely have company in writing the article; other Wikipedians may join in and try to help you. Often their help will be as simple as correcting typos, categorizing the article, or formatting the article to give it a consistent "look and feel" with related articles. With more involved editors, you may wish to discuss the article's scope, organization or emphases on its talk page, which is found under the discussion tab at the upper left of the article. More detailed suggestions for collaborative writing are given at the end of this tutorial.

Adding links, categories, images, and references

Aside from the text, four elements are important in improving a Wikipedia article: links, categories, images and references.

Internal and external links

Links are called "internal" if they point to another Wikipedia article and "external" otherwise. Wikipedia encourages internal links for relatively unknown topics mentioned in the article. If readers don't understand a given term in a sentence, they may click on the link to get a quick overview before returning to the original article. This is one reason to make the lead section of an article an easily accessible summary of the entire article.

Wikipedia articles typically end with a few standard sections. The first of these is the “See also” section, which links to other articles in related fields that were not mentioned in the main body. This section is usually followed by the "Notes" or "References" section.

The final section of a typical Wikipedia article is the “External links” section. These external links are generally not those cited in the References section; rather, they are often online tutorials or other educational resources that complement the Wikipedia article. There are usually between 5 and 15 external links, although fewer and more numerous sections are sometimes seen.

Images: Illustrating the article

A three-dimensional image of the proteasome

Wikipedia articles are generally well-illustrated, even when the text is relatively poor. Many articles have one image for every few paragraphs of text.

The most important issue for images is their copyright status. Images in the public domain, or released under one of the free licenses compatible with Wikipedia, can be uploaded at will. In other cases, the uploader should own the copyright and be willing to release the image. The various issues surrounding image copyright on Wikipedia are discussed here and at the linked articles.

Incorporating images into an article

For more details, see the tutorials Wikipedia:Picture tutorial, Wikipedia:Graphics tutorials, and Wikipedia:How to improve image quality.

The syntax for images is described here.

To include an image in an article, add the image file name between double square brackets, preceded by the word “Image:”, e.g., “[[Image:Proteasome.jpg]]". The image can be aligned with the right or left margin using those words as arguments, as in “[[Image:Proteasome.jpg|right]]"; right alignment is the default. Wikipedia's image policy strongly encourages using the 'thumbnail' size for most images, as in “[[Image:Proteasome.jpg|right|thumb]]", but an image that requires larger display, such as a map or diagram, can be scaled by specifying a pixel size, as in “[[Image:Proteasome.jpg|right|250px]]". Captions are desirable, and are added at the end, after another vertical bar, as in “[[Image:Proteasome.jpg|thumb|A three-dimensional image of the proteasome]]", which appears at right.

Creating graphs, diagrams and animations

See also Wikipedia:How to create graphs for Wikipedia articles.

Graphs and diagrams are used frequently to illustrate concepts in Wikipedia's science articles. The preferred format for such images is SVG (Scalable Vector Graphics), since such images retain their precision even at different sizes. Alternative image formats include PNG, GIF and JPG.

Animations are also welcomed at Wikipedia, such as the animation of the conformational change between the R and T states of hemoglobin. However, large animation files are discouraged, since they require a long time to download. Typically, image and animation files should be fewer than a few megabytes.

Providing references and footnotes for the article

Full instructions for adding references to Wikipedia articles can be found here and here.

Wikipedia's authority as a reference source derives mostly from its citations to the scholarly literature; hence, accurate references are essential for the quality of Wikipedia's articles. The density of citations in the best Wikipedia articles (Good articles and Featured articles) is typically 3 citations per kilobyte of readable text, which is roughly equivalent to that found in scientific review articles.

A review of Wikipedia's Featured articles shows that the prevailing form of referencing in Wikipedia is what Wikipedians refer to as "inline citation"; these are small numerical superscripts that link within the page to the reference section at the bottom of the page.^[1] Such references may be added at a point in the article using an HTML-like tag :

<ref>...text of the reference...</ref>

To make the text appear at the bottom, you must add a "references" tag to the References section near the bottom of the article, e.g.,

==References==
{{reflist|1}}

Using this approach, the references are automatically numbered in order of their appearance within the text.^[2]

In some cases, you may wish to cite a reference more than once. This can be done by giving the reference a name at any of the places it is cited

<ref name="Thompson">...text of the reference...</ref>

At the other positions where this reference is cited, the whole reference need not be written out; instead, you can write^[1]

<ref name="Thompson" />

Citation templates

Several citation templates have been developed to enable a uniform format for references across articles. These templates have the form

{{cite journal
| author= [[David Baltimore|Baltimore D]]
| year = 1970
| title= RNA-dependent DNA polymerase in virions of RNA tumour viruses
| journal= [[Nature (journal)|Nature]]
| volume= 226
| number= 5252
| pages= 1209–11
| pmid= 4316300
}}

which appears as

Baltimore D (1970). "RNA-dependent DNA polymerase in virions of RNA tumour viruses". Nature. 226 (5252): 1209–11. PMID 4316300.

Different templates are used for different types of sources, such as journal articles, book chapters, and books. Such templates can be written automatically using the freely available Zotero software or this server. Zotero has the advantage of maintaining a database of references, similar to the proprietary software EndNote or Reference Manager, and can be used to format scientific journals.

Developing the article into a Featured article

The highest level of Wikipedia article is the Featured article. In principle, these articles have been vetted by the active Wikipedia community for excellent writing, accurate and complete coverage, and for consistency with Wikipedia's style guidelines. A complete list of the criteria can be found here. Each candidate for Featured article undergoes a detailed scrutiny, often lasting weeks, before it is certified as Featured — or not. Only Featured articles may appear on the Main Page of Wikipedia, which gives them vast exposure to the world at large (typically 5 million page views per day) with commensurate impact for scientific outreach.

To reach this level, the first step is to write a comprehensive, well-written, well-referenced and well-illustrated article. The topic can be quite specialized, such as a single organism, single organelle or even a single type of enzyme; it is not necessary to write only on general topics such as bird or dinosaur. The requirement for excellent writing is a common stumbling block, but many Wikipedians are willing to assist experts in making their prose flowing and accessible to non-experts, while maintaining its accuracy. Another common stumbling block is the requirement for consistency with Wikipedia's style guidelines; again, Wikipedians have formed groups such as the FA-Team to assist with this.

The instructions for nominating an article as a Featured article can be found here. During an article's candidacy for Featured article status, Wikipedians can express their opinion whether the article meets the criteria or not, by indicating Support, Neutral, or Oppose. Frequently, improvements are made to the article in the process. Approval as a Featured article is governed by consensus rather than a vote: the directors must be satisfied that all valid objections have been overcome.

Tips for collaborative writing

This brief tutorial just scratches the surface of Wikipedia; there's lots left to learn! Fortunately, Wikipedia is full of friendly, knowledgeable people who will help you navigate its highways and byways.

Your conversations and collaborations with other Wikipedians are a key part of the pleasure, and the strength, of Wikipedia. You'll enjoy the company of fellow enthusiasts and benefit from their often complementary expertise; you won't have to do everything yourself! Here are some tips to help you succeed brilliantly in Wikipedia society:

Develop a network of friends who will help you copyedit, peer-review, and generally improve your articles. WikiProjects are a good starting place. As Tim says, do good turns, and you'll receive the same. One of the most helpful services academics can provide is steering other editors towards the best sources to use for an article and helping them gain access to those materials.

Be open to different perspectives and emphases A cell biologist might have a different view of a topic than, say, a physiologist, a biochemist, a physicist, or a medieval historian; but together they can find common ground. The article doesn't have to be perfect. Be willing to accommodate your fellow Wikipedians, and remember that you do not write for yourself but for the public. Most Wikipedia editors are not academics and therefore the feedback you will receive is not always similar to what a professional peer reviewer would offer. However, what these non-professionals can offer you is a sense of how well you have communicated your basic ideas to a lay audience.

Stay grounded in facts and reliable sources. Agree on a common nomenclature and descriptive variables. Be cool and professional, even if others are not.

Make use of article talk pages and other fora If you are writing an article with a group of other people, it is best to discuss the structure of the article, the sources for that article, the prose, and the images on the article talk page. WikiProjects also help articulate the principles behind a good article in their particular subject areas. The most fruitful discussions reflect a sharing of knowledge, brainstorming, a willingness to compromise, and the excitement of discovering the best way to present the information to the reader.

Be willing to adapt to Wikipedia culture Wikipedia is a community like any other: it has explicit expectations of its users laid out in the five pillars but it also has unwritten social taboos and internal politics. Writing with other editors means that you will have to navigate these expectations and unwritten rules to some extent. No one expects new editors to know the internal workings of Wikipedia's community, so mistakes are inevitable; however, it is crucial to understand that there is an entire society behind the encyclopedia.

References

^ ^a ^b This is the first example of a reference.
^ This is another example of a reference.

All the participants should be listed in the Category:ASCB 2008 Wikipedia workshop participants category. Those needing help will be in Category:ASCB 2008 Wikipedia workshop participants needing help, and should have a template that looks like this:

Wikimania 2008 talk on the quality of the English Wikipedia's scientific articles

Since January 2007, my students and I have investigated the scope of the English Wikipedia and the quality of its scientific articles. Part of our assessment involved quantitative analyses of hundreds of randomly selected articles from Wikipedia, whereas another part involved asking nearly 100 tenured professors at research institutions to review Wikipedia science articles in detail. Our data provide some evidence with which to address commonly held misconceptions about Wikipedia, and to appreciate where Wikipedia is and how far it has yet to go. I presented my students' work at Wikimania 2008 in Alexandria, together with some suggestions for the community of Wikipedians. You can see a video of the presentation here. However, the file is almost half a gigabyte (over 500 MB), and may take a long time to download. I'll be submitting our work for publication, and once the article is accepted for publication, I'll make the raw data, reviews and methods publicly available without restrictions.

Teaching Resources

As part of my teaching, I've been developing public-domain resources for teaching biochemistry, particularly protein science. Some example quiz problems are given here. I've written several hundred such problems and I would be happy to see them used more broadly. I would also appreciate any suggestions for improving them.

JavaScript programs

I've begun to learn JavaScript, often called the "assembly language of the web" and very helpful in making scripts for Wikipedia. My long-term goal is to make a WYSIWYG editor for Wikipedians, which is an urgent but difficult need for Wikipedians, according to the discussion at Wikimania 2008. As a warm-up exercise, I've made a few fun scripts that you might enjoy. To install them, you can add (for example) "importScript('User:Proteins/striparticlelinks.js');" to your monobook.js subpage under your user name, as you can see at my own user page. These scripts are still being developed, so they may have bugs. Alerts to such bugs and suggestions for improving the scripts are always welcome.

JavaScript programs for Wikipedia

Check for compliance with the Manual of Style

User:Proteins/mosheadcheck.js

The Manual of Style (MoS) is sometimes hard to keep entirely in one's head, especially as a newbie. This convenient little script checks an article for possible violations of the MoS guidelines on section headings. You can try it out on this MoS nightmare.

Analyze chemical reactions

User:Proteins/chemicalreactions.js

This draft script analyzes chemical reactions, checking whether they're balanced and whether mass is conserved. You can test it out in this sandbox.

Pose study questions to the reader

User:Proteins/studyquestions.js

This draft script poses study questions to the reader. You can test it out in this sandbox.

Sort unordered lists

User:Proteins/sortunorderedlists.js

This script adds buttons to all the unordered lists with more than one item. Clicking that button sorts the unordered list alphabetically.

A great use for this script is in ordering the output of the Special:WhatLinkshere page. The output is normally ordered by the pageID of the article in the database. This makes it hard to search through for humans. PageID's corresponds roughly to the order in which articles were added to the database, but not entirely, since a new page ID is assigned when the article is moved, as happens occasionally, esp. in mergers and some forms of vandalism.

Here's a convenient link for obtaining 1000 article-space links to a given article:

Super-charged WhatLinksHere

Super-charged WhatLinksHere (secure server)

The script should sort these results in under 15 seconds, depending on your browser and computer. Google Chrome appears to be fastest in running this script, although systematic comparisons have not been made. If the browser warns that the page has become inactive when sorting an extremely long list, please allow the script to continue; it will finish eventually.

List redlinks on a page and provide search links to major databases

User:Proteins/listredlinks.js

This script creates a new section at the top of an article, listing the remaining redlinks in the article and providing search links to Google, Google Scholar and various other databases. The underlying article on the Wikipedia database is unchanged. The search links resemble those of the {{Findsources}} and {{Search}} templates, but I tried to make them slightly more user-friendly and also biased towards science. Suggestions for new databases would be welcome. It would also be possible to make several versions of this script, for example specializing the databases for different groups of users.

Follow a random link on a page (good for random FA, random GA, etc.)

User:Proteins/followrandomlinkonpage.js

This script randomly selects a link on the present page and opens it in a new tab or window. The script is invoked by clicking on the "Follow a lucky link!" message in the "navigation" portlet, which is in the left-hand column, just below the Wikipedia logo. Multiple random articles can be spawned by clicking multiple times.

Wikipedia already has a "Random article" function found in the same portlet. However, that function takes you anywhere in the English Wikipedia, which now has 6,927,597 articles. It might be more fun and more useful to be able to choose randomly from a more restricted set, such as the set of Featured Articles, the articles in a category, or a list made by the user.

A user can gradually "diffuse" away from the original page by iteratively following a random link on each successive random page. I think it's a popular pastime in paper encyclopedias. For this reason, I almost named this script "Get lost in Wikipedia", but "Follow a lucky link!" sounded more fun and positive. A minor modification of this script would allow users to follow a random link in the "See also" list, but putting all links in play seemed better.

Another modification of this script would allow users to generate statistics on large sets of articles; as such, it may be useful to WikiProjects and researchers of Wikipedia.

Expand Wikipedia acronyms for newbies

User:Proteins/expandWPacronyms.js

Various acronyms such as WP:OR, WP:NOT and WP:V are used as a convenient shorthand among long-time contributors to Wikipedia. However, these acronyms have the disadvantage of making Wikipedia seem unwelcoming to newbies, as described in the essay Wikipedia:WTF? OMG! TMD TLA. ARG! This script seeks to reconcile the convenience of these abbreviations with the comfort of newcomers. When invoked, the script adds a parenthetical explanation to every such hyperlinked abbreviation on a page. Long-time contributors can use the abbreviations and need not invoke the script, whereas newbies can invoke the script when perplexed. Thus, different editors can see the same page in different ways, in the way most comfortable to each.

Check whether the images on a page have alt text

User:Proteins/checkALTtext.js

This script determines the percentage of images on a page that lack alternative text. Alt text is what is read to visually impaired readers of Wikipedia in lieu of the images. This script also blanks images that lack alt text, to help editors think of good alt text by considering the essential elements of the image.

Online help messages

User:Proteins/helpmessages.js

Wikipedia has a rich repetoire of Help pages, but they can be daunting for newbies to read through. It can also be hard for newbies to find out which one pertains to their question or quandry. Wikipedia also has online users who will help answer questions, but newbies might not know of them or how to find them.

Therefore, it might be helpful to have something inbetween, a automated system by which users can type questions into a text box, be given a short answer, and be directed to pages that give a fuller answer. This script (under development) is a step towards that goal. Try typing in a question about boldface type, for example.

Translate interwiki links into English

User:Proteins/translateinterwikicodes.js

This script translates the interwiki links in the lefthand column into English. This is helpful for screen readers such as Fire Vox, which skips over words written in alphabets it doesn't recognize and gives no hint of their presence. Many English-speaking Wikipedians may also appreciate being able to recognize the interwiki languages at a glance. The access key is "i".

Summarize diffs

User:Proteins/quickdiffs.js

This script produces a summary of the differences between two versions of a page. Especially helpful for accessibility reasons.

Summarize AfD !votes

User:Proteins/summarizeAfD.js

This script counts the different types of !votes on an XfD page. The first pop-up window gives the counts of each type (such as Keep, Delete/remove, Merge, Redirect, Note, Comment or other); following windows list the users who voted each way. The access key is "a".

Assist screen readers by stripping out hyperlinks

User:Proteins/striparticlelinks.js

This script strips out hyperlinks from an article that are likely to interrupt its smooth reading by a screen reader. Screen readers such as Fire Vox highlight hyperlinks by pausing and saying something like "LINK". Wikipedia prose is dense with hyperlinks, which makes the reading laborious; stripping out links improves its flow. The access key is "s".

To hear articles read aloud, you can install a screen reader and this script. To strip the links from a given article, you can click on the "strip links" tab near the top, or type the keyboard shortcut ALT-Shift-S in Fire Fox, Chrome and Internet Explorer (see Wikipedia:Keyboard shortcuts for the prefix for other browsers). Click at the beginning of the prose you'd like to read and start your screen reader (Ctrl-Shift-A in Fire Vox). The stripping may take a few seconds, roughly 1 second for every 100 hyperlinks removed. As a bonus, the script numbers the images on the fly, "Image 1", "Image 2", etc. As an aside, I'm not endorsing Fire Vox as a screen reader; there are many good screen readers available.

Outdent indented text, while coloring and labeling it

User:Proteins/outdent.js

The indenting created by placing colons at the start of the line in MediaWiki software is actually quite complicated in HTML, and causes accessibility problems. The complex nesting of discursive lists required to make that apparently simple formatting makes reading tiresome for people using screen readers, which describe each level of each discursive list. This script outdents all such indented text but does not affect true discursive lists that have a DT element. To keep track of the indenting level, the script colors the outdented text according to its indent level and prepends a short string such as "(Indent 2)" to make the indent level audible with screen readers. The access key is "o".

Please try the script out and let me know of any bugs that you encounter. Sighted people may enjoy the script as well, since over-indented text (such as level 14, which happens surprisingly often) is sometimes hard to read. Suggestions for improving the scripts are welcome, as with all my scripts.

Generic geotag script

User:Proteins/genericgeotagscript.js

This script reads the latitude and longitude encoded in an article. This toy script is a stepping stone to several other scripts, such as displaying a map of the stars visible at that location on a given day at a given time, or creating lists of animals and plants that might be found in that vicinity.

Analyze article structure: the distribution of prose, images,...

User:Proteins/articlestructure.js

This script analyzes the distribution of prose and other elements within an article. It also checks for jumps in heading level, such as an illegal H1 heading (=Really important section=) or jumps in heading level, such as placing an H4 section (====Tiny script====) after an H2 section ((==Normal script==) without an intervening H3 section (===Medium script===). Even some Featured Articles have such jumps! Such jumps are not only a Manual of Style issue, but also make articles less accessible, at least as I understand it. If you try it out here, you'll see a jump in this very section. The access key is "g".

While testing my script on Featured Articles, some random pages and some not-so-random, I've discovered numerous pathologies of articles that can trip up prose-size scripts, such as lists, quotes, PRE-tagged text, indented text, poems, special characters such as non-breaking spaces, and so on. I gathered many of them into User:Proteins/Prosesize_script_acid_test.

Possible extensions

Show CDF plots of the prose per section to highlight visually the sections that are thick with prose; can be made accessible using a chirp, by varying frequency (y-axis) versus time (x-axis). By playing the two limiting values as constant tones, even small discrepancies could be detected as beat frequencies.
Plot the evolution of article parameters over time, perhaps with markers for the median values for Featured Articles and Good Articles. Use the same frequency vs. time trick to make the plot accessible.

New ideas for scripts

Script to check for overlinking and other FAC violations.
~~Add button to all unordered lists to sort them alphabetically, or by other criteria. Generally useful, but good for easier searching in Special:WhatLinksHere.~~
Drag-n-drop editor that works on the Table of Contents, to allow whole sections to be re-arranged within an article, or to make it easy to create a new section at a specific point in an article.
Turn on "Add image" icon before every paragraph, analogous to HotCat. Add (±)(−) to existing images.
Turn on "Add reference" icon after every sentence. Trigger pops up a form window that allows editors to type the needed elements for a well-formed reference into labeled boxes.
Make analogous "Add Table" form, after every section heading.
Allow easy surfing of the relevant images in the Commons category; have each image expand upon mouseover for visibility.
Clicking on the Enlarge button of thumb images to generate a copy of that image that can be moved around and re-sized at will to reconcile the needs of article layout (favors small images) and visibility (favors large images). An accessibility issue.
Include Lists of Figures, Images and Abbreviations next to the Table of Contents
Incorporate normally hidden glossary into technical articles that floast next to where the reader is, so that they can keep track of technical terms as they need them. Alternatively, incorporate hidden triggers into all instances of specific technical words, so that the right event would trigger a popup window with the definition and a hyperlink to a page that explains more.
allow more flexibility in sortable tables; sort then change layout on the fly
Some ideas for visualizing/navigating sets of interrelated articles exploiting the <imagemap> tag. Make it easy for editors to make their own imagemaps
~~Random featured article, random good article, random article within a category or hyperlinked on a page~~
slider button to scroll through animations frame-by-frame; could be used to visualize evolutions, field densities (set iso-levels) and flows such as historical migrations
activate GIF animations onmouseover
make the left-hand column customizable
controls to adjust the colors of images, or even of individual elements in images, for color blindness and other applications
flesh out tiny leads in otherwise full articles by automatically generating a summary in an alert window, by combining topic sentences from section paragraphs. Perhaps do likewise for individual sections when they're clicked on in the TOC.
more support for music and sound; generate music from score
need to add equivalent to ALT for Deaf readers?
include Watchlist tracker (like a stockmarket ticker) at the bottom of the present screen to monitor the latest N changes in an editor's Watchlist. Could be really annoying.
modified Watchlist that describes not only the latest change, but the recent frequency of edits and rate of change in bytes; alerts editors to rash of activity instead of one-off vandalism
JavaScript package that offers plotting powers
allow readers/editors to customize their workspace for pleasure and efficiency
Given a geotag (latitude and longitude), generate an image with two sliders of what the major stars would look like there. The sliders would control the time of day, and the day of the year. Have options for different calendars and different projections of the celestial hemisphere into two dimensions.
Given a geotag, generate clickable image maps of local geology, plants, animals, and local sites. Akin to Google Maps.
link images into a single structure to allow "motion" in multiple dimensions. For example, allow readers to "zoom in" to see substructures of a cell in arbitrary detail, or to "zoom out" to see the context of an animal in its ecosystem. Allow readers to travel through time, to see causes and consequences, such as the evolution of animals or the motion of continents in geological time. Could be cool; other dimensions or networks are possible. Similar to the animation slider idea above. Probably needs to be developed within the MediaWiki software.
redlink scripts: (1) list them, (2) automatically search Google for externally links on them or relevant free images
replace "edit", "history", etc. tabs with images; or eliminate them altogether for specialized purposes

Other random ideas

Write sequence alignment method that is cyclic, i.e., that minimizes the differences between successive sequences including the first and last sequences. This allows one to make an animation of the changes, insertions and deletions. This approach wouldn't be good for showing the phylogeny, but it'd be great for showing the variable segments. Such animations might be educational for the snRNA articles of the RNA WikiProject.

[test_ref-1] This is the first example of a reference.

[another_ref-2] This is another example of a reference.

[1]

[2]