Dunn:Tools/Wiki Tutorial

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<owwmenu font="calibri, helvetica, sans-serif" bold="1" color="black" bgcolor="white" hovercolor="white" bghovercolor="DodgerBlue" topFontSize="11.5" fontSize="9" pagewidth="800" image="Dunnminimenu.PNG" lab=""> Home=#, Home=Dunn, Recent Updates=Dunn:Recent Updates People=#, People=Dunn:People Projects=#, Projects=Dunn:Projects, Publications=Dunn:Publications, Support=Dunn:Projects/Support Blog=#, Blog=Dunn:Education/Biophysics Education Blog Education=#, Education=Dunn:Education, Teaching=Dunn:Education/Teaching, Outreach=Dunn:Education/Outreach, Tools=#, Tools=Dunn:Tools, Wiki Tutorial=Dunn:Tools/Wiki Tutorial, Protocols=Dunn:Tools/Protocols, Calendar=Dunn:Tools/Calendars, Contact=#, Contact=Dunn:Contact, Openings=Dunn:Contact/Openings


Setting up your User page

  • The Openwetware (OWW) site has a great page on creating this.
  • This other lab has a good list of things to try when setting your page up.

Editing Existing Pages

Adding Headers and Bullets

  • For me, the best way to post notes on the wiki is by using bullets. Typing a star (shift+8) at the beginning of a new line will give you a new bullet.
  • Typing double star underneath a line with a bullet will give you indented bullets:
    • <----- See?
  • You can continue this trend as you please.
  • The headings and subheadings within a page are arranged in the same way with = > == >===
    • Notice how the wiki will automatically start placing shortcut links at the top of the page for each header/subheader that you create! (If the page requires a lot of scrolling).

Storing/Accessing Files

  • Before going into details of how to do the following, I would like to suggest that before you hit the upload/submit button that you either:
    • Rename your file so that others can identify it as being yours and a date might help or
    • Use the comments box to leave this type of information so that it is easily identifiable. For papers, a summary might be good here as well.


  • Click on the 'upload file' link on the left sidebar (under 'toolbox').
  • Follow the instructions onscreen to upload the paper. Read the information here as it will cover most of the tips that I will highlight below (also before you hit the 'upload' button, notice that there is a little 'summary' box where you can describe the file...this might be handy for searching through files later on). Now keep track of the title of the file after it has been uploaded ie. image:Koch et al. 2002.pdf so that you can call the file for when you actually want to use it.

Accessing Files

  • A great demo of how to place a link that will access your file (or even display the file) is found here.
    • Most things that you will upload will have the word 'image' in front of it. Only picture files should retain the word 'image' if you want to post them on a page. For any other file (ie. .doc, .xls, .pdf etc...) use the word 'media' in front (type it in manually when you want to retrieve it on a page), for example 'media:Koch et al. 2002.pdf' will work appropriately.
  • Now go back to the page where you wanted to insert the file and edit the page. Use double brackets [[]] to close in the name of the file that you will upload. A good example of how to do this is found here (under 'storing files' heading).
    • Notice the use of the | character (shift+ button right above enter button on keyboard) whenever you want to add text to the link. It can also do a few other things for images like adjusting size and position on page.
  • After uploading the paper as you wanted click 'save' at the bottom of the screen. An uploaded paper will look like this if you didn't link specific text to the file (I uploaded one of Alex's papers to show an example:
    • Media:Dunnnsmb.pdf.
    • Here is the same file with text linked. Click on 'edit' up top if you'd like to see what I typed to get different results (copying and pasting the text that someone else wrote on a page is a good approach to making the wiki look the way someone made it look by the way).

Linking to websites

  • Simply copy the address that you want to link and paste it inside single brackets.
    • ie. [1] or add a word right after the address but before the second bracket (separated by a space only) to link the address to a specific word:
    • ie. see?

Making Comments on a Page

  • Identifying a comment by a specific person is as easy as typing four consecutive '~' characters. This will give the name of the user, and the date when the comment was made (three of those will only give the name). ie:
  • Ramalldf: Just name
  • Ramalldf 23:08, 8 May 2009 (EDT):Name and date.
  • I'd strongly encourage using this when editing a page created by someone else as it makes it very easy to find changes made to a page by someone else. It is also seen as common etiquette on OWW to place your signature next to your changes.

Adding Mathematical Formulas

  • I haven't played around with this much, but it looks very straight forward. Here's a page that covers it in-depth. Here's an example:

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \int\limits_{1}^{3}\frac{e^3/x}{x^2}\, dx}

  • To make things easier for you, in the edit box, there's a 'math formula' button where the bold and italics buttons are.

Embedding Apps

  • You can add things like calendars, and documents to a page. It is easiest when an online application gives you the direct code to embed the app. For example, our lab has youtube, scribd, and google accounts, all of which offer code to embed files. The simplest way to embed the file is to simply paste the ENTIRE embed code in between <html> and </html> commands. For example:

<html><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/Xo9bwQuYrRo&hl=en_US&fs=1&color1=0x402061&color2=0x9461ca"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Xo9bwQuYrRo&hl=en_US&fs=1&color1=0x402061&color2=0x9461ca" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object></html>

  • By flanking this entire code with <center> and </center> you can center the app on the screen:
<html><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/Xo9bwQuYrRo&hl=en_US&fs=1&color1=0x402061&color2=0x9461ca"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Xo9bwQuYrRo&hl=en_US&fs=1&color1=0x402061&color2=0x9461ca" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object></html>

  • The Dunn lab website uses the embedding feature a lot so you can look at different pages and see things like pdfs, calendars, and powerpoints embedded as well.
  • An additional feature that you can use is the iframe feature that allows you to embed entire webpages onto yours. I don't use it very much and am not a pro at it, but Anthony Salvagno from the Koch lab has mastered this feature so you can check out his notebook and get good tips about how to do this (ie. this Friendfeed page).

Pubmed Footnoting

  • Ramalldf 01:31, 1 July 2009 (EDT):This is really cool! It will basically place all of the relevant information about the paper you're citing simply by entering the pubmed id # in the way that I have below [1]. Thus, with the first brackets you're basically placing the footnote # and with the second set of brackets, you tell it where you want the citation to go (in my example, under the references section). I wouldn't play around with trying to arrange the numbering at this point (notice how it may not be in order?), it can get really messy really quickly. As long as the character or word that you assign the citation to matches the one you want in the 'biblio' brackets you should get the correct citation.


  1. Pierobon P, Achouri S, Courty S, Dunn AR, Spudich JA, Dahan M, and Cappello G. Velocity, processivity, and individual steps of single myosin V molecules in live cells. Biophys J. 2009 May 20;96(10):4268-75. DOI:10.1016/j.bpj.2009.02.045 | PubMed ID:19450497 | HubMed [Diego]

Creating new pages and templates

New Pages

  • You can create a page by editing any exisiting page and doing the following. It will only become a subpage if you assign it to be as described below, but until I find a way to create a new page (ie. like a sandbox?) without having to go and edit a random page, you should do the following:
  • So I've found out that you can create pages in the following way:
    • Two of these brackets [[ ]] with a word in the middle will create a new page wherever you are. Unfortunately, the wiki has the potential to become HUGE, so in order to keep track of the locations of these pages you should try to create a link back to the page where this one originated from.
    • In order to do this you must enter the name of the new page with a "/" mark in between it and the page that brought you to it. For example:
 Lab News/Editing wiki
  • "Editing wiki" is the new name of my page. It will be red until I click on it and begin typing stuff and saving it.
    • If I want the link to not look like "Lab News/Editing wiki" but instead want the link to have another word leading to the link, then I will put whatever this sign is "|" after the name of my new page and type the word after it. ie.:
  • This type of writing will work on any page that you want and even on the toolbar if you decided to change it (you must remember the name of the page of course, cause if it is not the same, then the wiki will create a new one).
  • You can link/access a page that you want either by copying down the url and inserting it or just by placing the name of the page in brackets.


  • Templates are preset components of a page that you can immediately insert into a page without having to type out the code (I think that's what it would be called...)all over again. You can create a template simply by typing what you want the name of the template to be inside curly brackets {{}}.
  • This will appear in red and basically looks like a new page that you can edit any way you want (so it can include text and/or pictures).
  • A great example of a template is the main menu template (notice used the url to retrieve instead of using the curly brackets because the curly brackets would've put the actual template on the page which is not what I want to do).
  • Anyways, the following is some advice about editing those. I don't know that much about these, but this is how I learned how to use the toolbar template which I found on the openwetware public wiki somewhere.


  • For a lot of templates you can adjust the size and colors of the components belonging to that template (ie. width and color of a box).
  • The colors that are available can be found in theselinks. Typing the name or number of the color as it appears on that page will allow you to change the color to exactly that one (think that its case sensitive).

Template Toolbar

  • The toolbar is a little different because some of the links that are created in it do not necessarily have the same code (brackets) to link to pages. You should be able to link to existing pages (or actually new pages) by just typing in the information you should still be able to link them to whatever page that you please.
  • For example, look at the code for "Template:DunnMainMenu" (click on 'edit' up top) and you should find the following:
  • This is the code that was set up by Bill to create those links that you've seen already. This is the ORIGINAL code for the template that tells the wiki to put the main menu template onto a particular page. Notice that in order to link the words that you see on the main menu toolbar (which are actually the same as on the "MiniMenuToolbar" template (above) to existing pages, you can just add the new page in essentially the same format as I showed you above (only without the brackets).
  • From now on, any changes made to the "DunnMainMenu" template will be copied and pasted to the "MiniMenuToolbar" template so that they agree.
  • People have the floating mini menu template on any page they want as long as they call the template by typing {{}} with the name of the template in between those mustaches. Here's an example.
  • Notice that when I put the link above, I only typed "/|example" in between the brackets. If you are already in a page and want to create a sub-page that will link back to this original page, then all you have to do is type "/New page name|Word that will show up as link" (all of this in between the brackets of course).
  • Putting the full name of page A in the code only applies when you are in page B, but are trying to create a link for a subpage C in page A (edit: I know that this is true for creating links from the template toolbars, but I'm not sure if this applies to regular pages...).

Final Notes on Editing the Wiki

  • A page can get completely lost if you don't place its link somewhere visible or if you don't make the new page as a subpage of an existing one.
  • Try playing around with it. Here's a page that describes some cool things to try out, and here's another tutorial.
  • Not all pages will have the easy to navigate main menu template or mini menu templates (though you can add them manually to your pages) so if you get lost somehow, the best way to get back to where you were would be to go back to the main page or go to the 'Recent Changes' link (both of which are on the top left of the sidebar).