Computational lab, Ecol553 (Genomics)

Main course page

Useful Links:
ICE (hpc)
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)
Link to book: Perl for Exploring DNA
Online regex tester

HPC information page
Applet SSH server for HPC
MySQL on amadeus

Week Reading / Links Lecture "notes" Exercises Extras
1 Intro to Excel class notes
excel sheet that covers
  the kind of material discussed
  in class (and more)
excel sheet for exercises
name list
numbers
named numbers
ranges
genome annotation
chart data 1 chart data 2
 
2 Genomics resources/tools genomics resources
bookmarks
blast queries
   
3 Amadeus (the unix server)
Unix tutorial (part 1: sections 1-5, 8, 10, 11)
  Class exercises / homework
kunitz_inhibitors
fly.IDs.txt
Solution to homework 1
SSH on Windows
WinSCP
Fugu (SCP for Mac)
Unix Crib Sheet
Unix Essentials
Another unix reference card
4 Genomics resources/tools     Guide to genomics tools (blast/alignment/etc)
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
  homework2
exercises from class
Supercomputer (using SSH or SCP/SFTP):
  ice.hpc.arizona.edu
  marin.hpc.arizona.edu

HPC information page

6 "Beginning Perl"   exercises from class  
7 "Beginning Perl"   exercises from class
Homework 3
Solutions to homework 3
 
8 "Beginning Perl"
  exercises from class
 
9     (notice - solutions for homework 3 are listed in week 7, above)
exercises from class
Homework 4
 
10 "Beginning Perl"   exercises from class
Homework 4 (final version)
Solutions to homework 4
 
11     Homework 5
Homework 5 (updated)
exercises from class
 
12 Chapter 8 - subroutines
Chapter 10 - modules
A very simple intro to modules
  exercises from class
Solutions to homework 5
 
13 BioPerl docs
    Docs for
v.1.4, the version on ICE.
    Use "SearchIO" for blast file parsing.
BioPerl wiki page
  exercises from class