BIOL368/F11:Week 12

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, November 30 at midnight PST (Tuesday night/Wednesday morning). NOTE that the server is on Eastern Standard time (EST), therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL368/F11" category to the end of your wiki page.

Getting to know your microarray data

The task for this week is to download and organize the microarray data corresponding to your paper to get it ready for analysis next week.

  1. Go to the ArrayExpress site for your data and select "view all available files".
  2. Download the following files:
    • Experiment ReadMe
    • sdrf.xls
    • Array ReadMe
    • adf.xls
  3. Then upload these files to the OpenWetWare wiki and then link to them on your individual journal pages. Only one member of your group needs to upload them, then both partners can just link to the same file.
  4. From the methods section of your microarray paper, you need to figure out the following:
    • What samples did they collect and use for the microarray experiment?
    • How many microarray chips did they hybridize in the experiment?
    • Which samples were paired to hybridize on the chip?
    • Which was labeled red (Cy5)? Which was labeled green (Cy3)?
    • How many replicates did they perform of each type?
      • Biological replicates are made from entirely different biological samples.
      • Technical replicates are made when one biological sample is split at a particular stage in the procedure and then carried through to the end of the procedure.
  5. Record this information on your individual journal pages. If you have this from your journal outline, you can copy and paste it into your new journal page.
  6. Using the sdrf.xls file, you need to then find the names of the files that correspond to the names of your samples from the paper. Make a list that says which file corresponds to which sample.
  7. The instructor will then show you which columns of data to copy into a new Master spreadsheet. You will upload this spreadsheet to the wiki and then link to it from your journal page.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F11:Class Journal Week 11 page. If this page does not exist yet, go ahead and create it.
  • Link to the shared journal entry from your user page; this should be part of your template.
  • Link the shared journal page to this assignment 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).


  • Did you do anything fun over Thanksgiving break? :)