BIO/CSC295 2011F, Class 19: Microarrays (2)

Overview:
* Mid-semester examinations.
* Projects.
* Project 9.4a.
* Debrief.

Admin:
* Candy
* EC for tomorrow's bio talk on sugar, biofilms, and stress relief.
* EC for ISO Food Bazaar
* EC for going to St. Norbert's in somewhere Wisconsin to support the volleyball team
* EC for swim meet tomorrow night at 6:30 in the red shorts pool
* EC for senior football game Saturday at 1pm
* EC for supporting Logan at the Aztec bowl somewhere in Mexico during
  finals week
* Distributed: Notes on the Project.
* Today's lab: Project 9.4a.

Each problem is graded on a 1-10 scale
In general, you did very well.  Sometimes you had difficulty counting.
"List three things != thing1, thing1 again, and thing2"
* We're happy to talk about how we graded
* But we don't like to do "You graded Joe differently than you graded me!"

Needleman Wunsch
    # Fill in all the other entries
    for row in range(1,len2+1):
        for col in range(1,len1+1):
            if (seq1[col-1] == seq2[row-1]):
               valMat = values[row-1][col-1] + actionValues['Mat']
               sym = 'Mat'
            else:
               valMat = values[row-1][col-1] + actionValues['Mis']
               sym = 'Mis'
            valIns = values[row-1][col] + actionValues['Ins']
            valDel = values[row][col-1] - actionValues['Del']
            val2Ins = values[row-2][col] + actionValues['Ins']
            val2Del = values[row][col-2] - actionValues['Del']

            value = max(valMat,valIns,valDel,val2Ins,val2Del)
            values[row][col] = value
            if (value == valMat):
                directions[row][col].append(sym)
            if (value == valIns):
                directions[row][col].append('Ins')
            if (value == valDel):
                directions[row][col].append('Del')
            if (value == val2Ins):
                directions[row][col].append('Ins2')
            if (value == val2Del):
                directions[row][col].append('Del2')

Sam also wanted 'update the print algorithm to deal with this new symbol',
but Sam was clearly overly optimistic on what you could do in ONLY
TEN MINUTES!

What should Joe do because she did not do as well as she hoped on the
examination?
* Come talk to Vida or Sam about what the difficulties were.
  * Or with questions on the things that you did not get.
* Be the little train that could "I think I can, I think I can"
* Demonstrate to Vida or Sam that they misgraded her.
* Consider your study technique and the problems you got wrong and
  think about what you need to change.
* Identify a (better) study group.
* Do unproductive things: Blame Chase.  Blame her cat.  
* Remember that it's only 10% of your grade and do better on other things.
* Encourage your alternate-discipline peers explain things better to you.
* Try to get hints about what kinds of questions will be on the final.

The Final Project
* You've built lots of skills
* Reading the primary literature
* Techniques for analyzing and approaching data
* Sources for data
* It's time to put together interesting biological questions and
  computational approaches.
* Most likely, taking advantage of data that are available on the Web.
* Biologists understand the problem domain and can suggest good 
  things to explore
  * Computer scientists should understand how to approach that problem
  * Both sets of students can look at the resulting "output data"

Some lessons from the lab
* Vida has a cool project
* join is nice because it deals with missing data (in a harsh
  way by deleting)
* We are likely to put the following question on the final:
  "Here is some important code from *your* project.  Explain
   what the code does and what role it serves in your project."
* Naive copy and paste can be dangerous
  * The line has changed since StC&V was published
  * The ORDER of lines is different