Computer Programming Languages and Algorithms in Bioinformatics 2010

 

Time: 24-28. May, 2010
Lecturer: Torgeir R. Hvidsten
Labs: Jenny Önskog

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

Basic syntax in Perl: PerlA4

Student evaluations: 2009, 2010

Time and place

Topics

Material
 
MONDAY
2010.05.24 		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
MA336, MIT 		Lab 1 (solutions)
numbers.txt
TUESDAY
2010.05.25 		9 - 12
KBF30, KBC
  • Introduction to Perl 2: hashes, data structures, references, subroutines, modules
 Lecture 2
(six slides on each page)
13-16
MA336, MIT 		Lab 2 (solutions)
microarray.txt
network.txt
WEDNESDAY
2010.05.26 		9 - 12
KBF30, KBC
  • Introduction to Perl 3: regular expressions, parallelization and running external programs and commands
  • Object-oriented programming
  • BioPerl
Lecture 3
(six slides on each page)
13-16
MA336, MIT 		Lab 3 (solutions)
hvidsten.com.html
genpept.txt
THUESDAY
2010.05.27 		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
MA336, MIT 		Lab 4 (solutions)
motifs.txt
FRIDAY
2010.05.28 		9 - 16
MA336, MIT
  • Perform one of the projects or bring your own project
  • Work individually or in pairs
Projects