Perl Programming with Application to Bioinformatics, 2 hp

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

Application form

Important dates

Application open: January 27

Application deadline: April 11

Confirmation to accepted students: April 18

Responsible teachers: Matthew Webster

If you don’t receive information according to the dates above, contact

Course fee

A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Course content

Course webpage

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.
To complete the course, students are expected to complete a short project, either from their own work or pre-defined.

Topics covered will 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.