Cancelled: Perl Programming with Application to Bioinformatics, 2 hp

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


The course has been cancelled!


Important dates

Application open: May 8

Application deadline: Prolonged to August 15

Confirmation to accepted students: August 16-17

Responsible teacher: 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 coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

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 Unix command line (e.g. Mac OSX or Linux) is a requirement for the course. 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. The course will also include practical computational exercises.

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

  • To get the maximum benefit from the course we would like you to
  • Be able to bring your own Mac or Linux laptop for the practical computational exercises. If you don’t have a Mac or Linux computer to bring please contact us at before you apply.
  • Be familiar in using the Unix command line (Mac OSX or Linux). We will not teach Unix in detail in the course and you will have considerable trouble to follow the practical computational exercises if you are not reasonably used to work in a Unix. Other course are available at SciLifeLab that introduce the basics in Unix.
  • 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.