Perl Programming with Application to Bioinformatics, 2 hp


National course. The course is open for PhD students, postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Application form

 

Important dates

Application open: June 24

Application deadline: September 3

Confirmation to accepted students: September 8

Responsible teacher: Matthew Webster

If you don’t receive information according to the dates above, contact eva.molin@scilifelab.uu.se

Course fee:

A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffe, lunches and course dinner).

Course content

Perl is the ideal programming language for biological data analysis. The course is for students with little or no prior knowledge in perl. Familiarity in using a command line would be beneficial. It is aimed at students who need computational skills to handle large datasets. The course will follow the book “Learning Perl”. It will consist of lectures to introduce all topics and computer assignments to be completed individually after each lecture. It will also include interactive sessions in a computer lab.

Topics include:

  • introduction to command line and writing perl scripts
  • handling scalar data, control structures
  • lists/arrays
  • subroutines
  • input/output
  • regular expressions and pattern matching
  • conditional operators
  • strings and sorting
  • loops
  • hashes
  • introduction to modules such as bioperl

By the end of the course, students should:

• understand and be able to implement all fundamental elements of Perl programming

• be able to write programs to perform common bioinformatics tasks

• be able to understand and debug Perl programs

• be competent using a Unix environment

Entry requirements

Basic Unix knowledge is a benefit but not definite requirement. It is strongly recommended that students read the course book “Learning Perl, 6th Edition” (Schwartz et al.) before attending the course.

Selection criteria

Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.