list of programs, files, and links

Notes for

• class 11: Perl and Databanks by Kaiyuan Shi: Materials here; ppt here
• class 10 : Introduction to Bioperl by Dr. Poptsova
• class 9: Possible Student Projects, see extract_lines script in examples, class_notes
• class 8: continue class 7, blastall, formatdb, discuss possible student projects
• class 7: regular expressions, gnuplot, blastall
• class 6: evaluating logical expressions, regular expressions, use of modules
• class 5: sort, hashes, glob and system
• class 4: more control stuctures, file input, subroutines, hashes
• class 3: Control structures, if , while, for, ARGV
• class 2: String and number manipulations, arrays
• class 1: UNIX / Mac OS X, accounts, vi, ssh, variable types, number manipulation, interpolation, assignments, evaluations
  

The amount of molecular data available in various data banks has exploded in recent years thanks to many completed and ongoing genome sequencing projects and due to many genome and proteome scale analyses. The number of programs used to analyze these data has increased with nearly equal speed.

The ability to handle large amounts of data has become a daily routine for many biologists; however, web based servers often are slow and cumbersome to use for repetitive tasks. Simple scripting tools provide an easy way for biologists to adapt programs to the tasks they want to perform. Perl is a computer language popular among biologists and bioinformaticians because it is easy to learn and allows to parse the complicated output of other programs. This course will not turn biologists into computer scientists, rather it will enable biologists to use computational tools more effectively.

• Update on how Perl is doing from his creator, Larry Wall:
  State of the Onion 2003 speech
  
• One hump or two? - Find out here
  
• Perl Poetry [i.e., poetic code that runs without errors when executed]
  
• Comprehensive Perl Archive Network [CPAN]
  
• BioPerl
  
• Very preliminary course outline