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Wiki lab practical

Before this lab, you should already have registered an account on and emailed your username to IanHolmes. If you haven't, please do this now at . Be sure to include the text "bioe131" in the subject line of your email. Your account should then be authorized for adding URLs and attaching files.

This lab and the associated homework are pretty straightforward. On the other hand, after the first year of running wiki-based homeworks, we found that there was a not-insubstantial administrative burden on the instructor, associated with loss of passwords and requests to reset them. Therefore, if you lose your password after registering and require a reset at any time during the semester, you will have 10% docked from your grade on this homework. Sorry if this seems draconian; unfortunately, without such a penalty, there's a Wikipedia:morale_hazard associated with choosing a forgettable password...

Please also be sure to read the note on TWiki webs below. All your user pages need to go in the Fall12 web or you won't have the necessary access privileges.

The purpose of this lab is to familiarize yourself with the general concept of a wiki, the specific syntax of (which is slightly different from the syntax of other wikis, such as Wikipedia, that you may have encountered) and the general layout of

Familiarization with wiki syntax

Read the following basic topics:

Browse the following advanced topics:

Using the Sandbox web, or your own home page, try the following:

  • add a short autobiographical description to your page (mentioning your interests in compbio, bioengineering or other biomedical science); feel free to remove unnecessary text from your page while doing this
  • create a bulleted list
  • create a numbered list
  • create a table of contents
  • experiment with various other stylistic elements, e.g. horizontal rules, colors, smilies, alternatively-formatted lists...
  • attach a photo of yourself to your page and display it inline (PLEASE make it a small image! i.e. under a megabyte! storage space on the server is limited...)
  • create a new page
  • view the revision history of a page
  • use the table plugin to create a table
  • use the Efetch plugin to auto-add a link to an article in Pubmed
  • use the Interwiki plugin to auto-add a link to a wikipedia page, like this: Wikipedia:Human_Genome_Project
  • use the Interwiki plugin to auto-add a link to a page in Genbank, Pfam, Rfam, Flybase, or some other biological database

Homework assignment

The following assignment should be completed on your own wiki page.

If you wish, you may alternately create a separate page for this assignment (including your name in the page title, e.g. "YourNameHomework1", to prevent name clashes with other students) and clearly link to it from your main page ("YourName"). You may then use access control to prevent others from viewing/plagiarising your answers. You can do this by including the following text to the new page:

   * Set ALLOWTOPICVIEW = YourName

Please do not block read access to your own main page! We want everyone to be able to read each others' home pages. If you want to be paranoid/competitive about homework assignments, and use access control to stop people from peeking, fair enough; but please do it on an assignment-by-assignment basis, i.e. create a new page for each assignment that you intend to protect.

Please note that is divided into different "webs". This page is in the "Teaching" web, containing all the lab descriptions, etc. You can see this from the navigation bar near the top of the page (just under the logo) and also in the URL for the page (note the form of the URL: Teaching/UsingWikiHomework). The only exception to the "web name is in the URL rule" is the Main web. That is, if you can't see the name of the web in the URL, then that mean's it's in the Main web, as you can see if you go to this page: IanHolmes. Note that the navigation bar at the top of the page still works in the Main web, so that's the most reliable way of seeing what web you're in. You may also note that the color scheme is different for the Teaching-related webs than it is for the Main web.

Your user pages should all go in the Fall12 web. If you registered using the "Register" link from one of the class pages, then your user page will already be in the correct web; otherwise, you will need to move it. If you put a page in the wrong web, you will not have the correct privileges for attaching files, adding URLS, etc. You can move a page from one web to another by clicking the "More" link at the bottom of the page, then selecting "Rename/move topic".

Credit will be given for appropriate use of TWiki syntax to enrich your assignment with stylistic elements such as lists, tables, links to external sites (or papers or databases), etc., as demonstrated by the exercises you did as part of the lab.

  1. Ensure that your home page (that's the main page designated by your username) includes a photo and a short piece of biographical text, as outlined in the lab.
  2. Add a short paragraph about ricin to your page. The paragraph should contain hyperlinks - use the Efetch plugin and/or the Interwiki plugin to include links to each of the following:
    • the Wikipedia page for ricin;
    • the Pubmed record for the 2010 Nature Biotech paper reporting the sequence of the Ricinus communis genome;
    • a Genbank or Swissprot entry for ricin protein sequence(s).
  3. Find any one Pubmed paper, Wikipedia article or Genbank entry relating to polio that interests you, and post a reference to it on your page (it is expected that this reference will be unique to your page; or, at least, that duplication of references for this part of the question will be extremely rare and unlikely).
  4. Also answer the following on your page:
    1. Describe four different types of cis - acting sequence signal;
    2. Using Google, Wikipedia and any other relevant sources, write a short description (1-4 sentences) of the following types of tool (including programs and databases) that are used in bioinformatics. Mention the main biological purpose or typical application of the tool, and name prominent examples of each type of tool (i.e. you should name actual programs that are widely used). Each type of tool comes in a pair: as an integral part of your description, compare and contrast the two tools in the pair. (For graduate students or extra undergraduate credit: within the space constraints, outline the main limitations encountered when using the tools in practice, e.g. accuracy, run-time, memory usage, etc.)
      1. gene function
        • Enzyme Commission numbers
        • the Reactome database
      2. representations of protein structure
        • Electrostatic surface model
        • Space-filling model
      3. genomics
        • Genome sequencing
        • Metagenomics
      4. RNA structure
        • RNA folding software
        • RNA design software
      5. computational biology
        • systems biology
        • molecular biophysics

-- IanHolmes - 27 Aug 2008

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