BIOL368/F11:Week 1

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, September 7 at midnight PDT (Sunday night/Monday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

User Page

Set up your individual user page on this wiki. OpenWetWare automatically fills in your user page with automated content that may not apply to you. You will need to delete any unneeded information from the automated content and add the following:

  1. Name
  2. Contact Information
    • E-mail address (I recommend that you use the "E-mail me through OpenWetware" link for this so that you don't make your real e-mail address public, and thus subject to spam.)
    • LMU snail mail address
  3. Education
    • Major
    • Expected graduation year
    • Upper division courses in biology, chemistry, math, and computer science that you have taken (including those in which you are enrolled this semester)
  4. Career interests and goals (if you know)
  5. What is your favorite aspect of biology and why?
  6. Feel free to customize your page in any way you wish, bearing in mind that this site is public and that you should present a professional face to the world.

If you prefer to keep your answers to the following questions private, please send Dr. Dahlquist an e-mail instead of including them in your user page:

  • Do you have any worries or concerns about this class at this point?
  • Is there anything else you would like the instructor to know?

For quid pro quo, do this as well:

  • Write one question that you would like to know about Dr. Dahlquist on her user talk page, and she will answer them there. Make sure to sign your question with the standard MediaWiki signature shortcut (~~~~).

Practice your Wiki Skills

Demonstrate all of the following skills in your user page. Find a way to integrate them naturally into the content (e.g., do not say "Here is an image." and put just any image on the page).

  1. Create a new Wiki page: [[new page title]]
    • When you include a non-existent link in a page (say, your user page), the software can tell that this page doesn't exist and colors it red instead of blue/purple. When you click on the red link, you are then given the option to edit (and thus create) the page.
    • I suggest you practice this by creating your Week 2 journal entry page. The name for the page should be in the format "username Week 2" (i.e., that is the text you put between the square brackets when you link to this page).
  2. Link to a page within our Wiki: [[BIOL398-01/S11:page title|optional visible label]]
  3. Link to an external Web page: http://address or [http://address visible label]
  4. Create an e-mail link: [ visible label]
    • Alternately, use the code for e-mailing through OpenWetware: [[Special:Emailuser/username|visible label]]
  5. Use headings: === title === (number of equals signs indicates heading level)
    • By convention, start your largest heading with two equals signs. The single equals sign is for the title of the page and is automatically created when you create the page.
  6. Create a bulleted list: *
  7. Create a numbered list: #
  8. "Comment out" your Wiki code: <!-- commented-out Wiki text --> When you "comment out" your wiki code, the code will be visible on the Edit page, but will not be visible on the wiki page itself. That way, you can keep a rough draft of a wiki page invisible until you are ready for it to be seen.
  9. Upload an image: Click Upload file then follow the instructions.
    • Use the image on your page: [[Image:exact-name-of-image-file]]
  10. Upload another type of file (such as .pdf): Click Upload file then follow the instructions.
    • Link to the file you uploaded on your Wiki page: [[Media:exact-name-of-uploaded-file|visible label]]
  11. Assign one or more categories to your page: [[Category:category name]]
    • This creates an automatic "table of contents" for the wiki. When you click on a category link at the bottom of a page, a new page opens giving you a list of all wiki pages that have been assigned that category.
    • Use the category "BIOL368/F11" to indicate your page is part of our class.
    • See the Special:Categories page to see a list of other categories you could use.
  12. Use the discussion (talk) page to make a comment. Wiki etiquette requires that you sign your comments with your "signature": ~~~~ (4 tildes in a row) (which gets converted automatically, for example, into: Kam D. Dahlquist 21:41, 5 November 2008 (EST) )
  13. Every time you edit a page (whether it is a content page or discussion page), enter a meaningful description of your change in the Summary field at the bottom of the editor. This allows other users to easily see (say via the Special:RecentChanges or history pages) what has happened to the page since they last visited it.
  14. Create a template for yourself and use it on your user page. Pages whose name starts with Template: are special — these are replicable blocks of wiki text that you can include in other pages. In fact, the Bioinformatics Laboratory heading and links at the top of this page are controlled by the Template:BIOL368/F11, and you can include it in any page by saying: {{BIOL368/F11}}. This will "expand" the template to its full contents on the actual page.
    • Create your own template [[Template:username]] and use it to create a set of navigation links that you will use in each week's journal entry. You should link to your user page, the assignment page, and any other links that will be useful.
    • Then use your template on your user page.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 1 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL368/F11" category to the end of the wiki page (if someone has not already done so).

Reflection Questions

  1. Had you heard about bioinformatics before signing up/taking this class? If so, how did you hear about it?
  2. What is one thing that you would like to know more about bioinformatics?
  3. What are your personal goals for this class; what do you hope to get out of it?
  4. Please feel free to read and respond to your classmates' answers.