BIO/CSC295 2009F, Class 25: Time for work on projects

Admin:
* Welcome back!  We hope you had a wonderful break and that you're ready
  for purgatory week.
* Projects are now due next Tuesday.
* We'll use class time this week to work on the projects.  
  * You are expected to show up to class.
  * I believe that I've updated the schedule appropriately.
* Sam remains behind in his grading.  Sorry.
* We'll talk more about other class work on Thursday.

Overview:
* Discuss in small groups
* Quick Summaries at 1:30
  * What your group has accomplished
  * How you want to use today
* Discuss
* Work
* Think
* Ask Questions

Shotgun Group
* Our goal is to ... build a useful shotgun sequencing algorithm and 
  apply it to some real data
* So far we have ... written an algorithm to "randomly" chop up a sequence to
  give ourselves test data
* Today we will ... write an algorithm to simulate restriction enzymes to
  give ourselves more realistic test data
* We need help with ... things 

Chou-Fasman Group
* Our goal is to ... improve Chou-Fasman by focusing on trans-membrane
  proteins (build a new table and test the efficacy of that table)
* So far we have ... found a database with information on trans-membrane
  proteins
* Today we will ... figure out how to parse the relevant data out of the
  text file
* We need help with ... parsing the text file

Replacement matrix group
* Our goal is to ... discover the evolutionary history of listeria
  bacteria; using BLAST to find phylogenetic data and come up with
  a model
* So far we have ... decided what we're doing; found the important
  gene
* Today we will ... figure out the direction for our odyssey; think
  about how much variability we'll allow
* We need help with ... working on it

MicroRNA group
* Our goal is to ... Find regulatory regions controlling the
  expression of MicroRNA
* So far we have ... found a collection of MicroRNA to study;
  written a program to translate format to FASTA; gotten ready
  to BLAST everything.
* Today we will ... figure out how to get upstream sections
* We need help with ... how to work with an entire genome, particularly
  how to figure out locations