Computer Programming Languages and Algorithms in Bioinformatics 2009

 

Time: 25-29. May, 2009
Lecturer: Torgeir R. Hvidsten

At the end of this course you will know how to :
- write and debug basic Perl programs
- select the correct algorithm design for a given problem and do time/space complexity analysis
- use online resources with Perl and use online Perl libraries and interfaces
- use Perl to pipeline other programs (e.g. BLAST) and parse output
- combined the above to solve practical Bioinformatics problems

Resources:
- www.perl.org
- www.cpan.org/
- BioPerl
- AtivePerl
- Open Perl IDE
- Beginner's Introduction to Perl

Student evaluations: 2009

Time and place

Topics

Material
 
MONDAY
2009.05.25 		9 - 12
KBF30, KBC
  • Introduction to programming: pseudo-code, examples of languages
  • Introduction to Perl 1: basic expressions, scalars, arrays, loops, conditions, file handling
Lecture 1
(six slides on each page)
13-16
DL-KB4B1, KBC 		Lab 1
(Suggested solutions)
TUESDAY
2009.05.26 		9 - 12
KBF30, KBC
  • Introduction to Perl 2: hashes, data structures, references, subroutines, modules
  • Object-oriented programming
  • BioPerl
Lecture 2
(six slides on each page)
13-16
DL-KB4B1, KBC 		Lab 2
(Suggested solutions)
WEDNESDAY
2009.05.27 		9 - 12
KBF30, KBC
  • Introduction to Perl 3: regular expressions, parallelization and running external programs and commands
  • Dynamic programming and sequence alignment
  • BioPerl: Running external programs
Lecture 3
(six slides on each page)
13-16
DL-KB4B1, KBC 		Lab 3
(Suggested solutions)
THUESDAY
2009.05.28 		9 - 12
KBF30, KBC
  • Basic algorithm design: exhaustive search, greedy algorithms, dynamic programming and randomized algorithms
  • Correct versus incorrect algorithms
  • Time/space complexity analysis
 Lecture 4
(six slides on each page)
13-16
DL-KB4B1, KBC 		Lab 4
(Suggested solutions)
FRIDAY
2009.05.29 		9 - 16
DL-KB4B1, KBC
  • Perform one of the projects or bring your own project
  • Work individually or in pairs
Projects