Computational lab, Ecol553 (Genomics)

Main course page

Useful Links:
Textpad - a decent text editor for programming.
Eclipse - a better programming editor ... but with a bit steeper learing curve (google for "eclipse perl" to see how to set yourself up for perl coding)
ActivePerl - a perl installation for Windows.
Cygwin - a Unix environment that runs in Windows (comes with Perl - use either this or ActivePerl, not both)
Online regex tester

MySQL on amadeus

Week Reading / Links Lecture "notes" Exercises Extras
1 relax pdfdoc
excel sheet used in lecture
excel sheet for exercises
numbers
named numbers
 
2 Amadeus (the unix server)
Unix tutorial (part 1: sections 1-5, 8, 10, 11)
handout
excel sheet used in lecture
excel sheet for the exercise
mouse genes
rat genes
connecting to biodesk
3 SSH secure shell
Unix Crib Sheet
Unix Essentials
handout for Tues
lecture notes for Tues
kunitz_inhibitors
fly.IDs.txt
Another unix reference card
4   lecture powerpoint nucleotide sequences
protein sequences
Blast Handout / Homework
Blast Homework Answers
blast on hpc
5 "Beginning Perl" by Simon Cozens:
  • Chapter 1, starting on 6th page of pdf (labeled pg 24).
  • Chapter 2, ignoring:
    • binary, hexadecimal and octal numbers
    • bitwise operators
  exercises from class
Homework 4
 
6 "Beginning Perl"   exercises from class  
7 "Beginning Perl"
  • Chapter 4 finish (and do all "Try It Out" exercises)
  exercises from class
Homework 5
Homework 5 solutions
 
8 "Beginning Perl"
  exercises from class
Homework 6
Homework 6 solutions
 
9     exercises from class  
10 "Beginning Perl"   exercises from class
Homework 7
Homework 7 solutions
 
11 "Beginning Perl"   exercises from class  
12 Chapter 10 - modules
A very simple intro to modules
BioPerl docs
    Docs for
v.1.2.3, the version on amadeus.
    Use "SearchIO" for blast file parsing.
BioPerl wiki page
  exercises from class
 
12 MySQL on amadeus
  Homework 8
homework 8 solution