BIO/CSC295 2009F, Class 03: What is Bioinformatics? (3)

Admin:
* Hand sanitizer is in the back of the room.  (Use it on your way out!)
* Apologies for the mixup on potential homework for today.  
  + You had nothing new due.
  + (We had initially planned to have you read each others' responses)
* For the next class, read Chapter 2 of Exploring Bioinformatics 
  + Bring questions.  
  + You don't need to do the chapter 2 Web exploration yet
  + You certainly don't need to understand all of the code in 2.5 and 
    beyond
* For the next class, finish (and turn in via email) the Web exploration on
  favism.
  * One set of answers per group
  * Email us both!
* Don't forget to go see Jillian in her "Almost, Maine" this weekend!
  * 7:30 on Saturday, 2 on Sunday at "The UCC Church across from Chung 
    Garden"
* Answers to some of your questions from the survey?
  * What food do you like best?
  * What ingredient do you like best?
  * Do you have pets at home?
  * What would you genetically engineer?
  * What do you like most about Grinnellians?
  * What student behaviors irritate you?
  * If you weren't in academia, what would you be doing?
  * Sam: Why CS?  Why Grinnell?
  * Vida: Why Bio?  Why Grinnell?
  * What research do you do?

Overview:
* Web exploration, continued.
* About algorithm design.
* Project 1.4 in Python.
* Folowup lab to Project 1.4.
* Reflection.

Web exploration clarifications:
* What gene do we want?
  * The gene for G6PD
* Vida says: 
  "Remember, in many searches, the second link returned is more useful
   than the first."
* Note: Rats are not human (although some humans act like rats)
* Yeah, we want 16+K of bases

Web exploration comments:
* Why?
  * It tortures the students
  * Get some experience navigating the databases
  * Shows possibilities of the information that's out there
    * What kinds of this information might you take advantage of
  * Bioinformatics is about data, these are useful data
  * Look, there are tools
    * Can we build our own?
    * Probably not the wicked neat 3D visualization system
* What's the hardest part?
  * Trying to get info from the primary literature
  * Evil faculty who won't let you use wikipedia and such ...
* Why else?
  * If we get diagnosed with genetic diseases, we can learn more about them
    from a reliable database

Time to think a bit about computer science
* What did our book say computer science is? (Or at least algorithms?)
  * Algorithms are sets of instructions for accomplishing a task
  * Computer scientists are supposedly really good at writing and
    criticising such sets of instructions
    * Particular instructions that can be "understood" by the computer
* Issues:
  * You have to be really exact- ambiguity is bad
  it hates everyone
  clearly understand the problem - understand biology
  multi  step process
  	strategy to solve problem
	design algorithm that encodes strategy
	write code
	CS are better at the isntructions we use

	translate strategy to code is not easy
	Ideal system - really you go back and forth

	short reading/lab - course web site
	Go to xbiopy -- projects -- 1.4  
	Look at code!
	Read then go to labs link 1.4
	exercises

* We'll continue this on Monday