Perl programming for biomedical researchers 2008

  • Material
  • Exercises


Using web-based tools for Bioinformatics research is very convenient for small amounts of data (e.g. less than 20 sequences). As soon as researchers want to analyse more sequences (from 20 up to thousands sequences or megabytes of data), the task becomes tedious.
The course aims at providing the basic knowledge of PERL scripting abilities to analyse large amounts of data by automating recurring tasks or by grouping several tasks into one program.
This course is organised for biomedical researchers and no particular programming knowledge is required, however some basic Unix/Linux computing skills would be of great advantage (see Audience).

At the end of the week, participants should know how to:
- Import/export data from/to Excel spreadsheets;
- Automatically Blast a given list of sequences and extract relevant information;
- Retrieve sequences from a list of AC/ID and convert them to different formats;
- Presentation and usage of some EMBOSS programs (e.g. Restriction Mapping, ...)
- Creation of a basic web interface to your own programs;


No particular programming knowledge is required in order to attend the course, however some basic computing skills would be of great advantage; As the programming practical exercises will necessitate the use of computer running the Unix/Linux operating system, you should already be familiar with the command line environment of such systems. While no advanced knowledge is required, you should be able to perform basic tasks such as logging into a command line terminal, navigating between directories and creating, deleting, and moving files. We will review (1 hour) the basic Unix commands during the first day of the course, but this will be brief, so as to be able to concentrate on the programming part of the course.

We will publish a self-assessment to help you test your Unix knowledge, and decide whether you have the prerequisites to optimally profit from the content of the course. In the mean time please have a look at the following tutorial: Chapters 1 to 6 are enough to learn the basics needed for the course.

If you do not have a Unix/Linux machine to practice the exercises of the Tutorial you can alternatively use:
  • The command line terminal of a Mac OS X computer.
  • Ask at the central computer administration of your University to get an account on a Unix machine and then connect to this machine from you personal PC using a terminal emulator like PuTTY or X-win32.


Course objectives

- ensuring familiarity with basic computer concepts and their everyday use in a biological laboratory setting.
- teaching them basic PERL programming enough to write simple scripts.
- acquainting the participants with existing programs and the way to join some of these together using small scripts.
- giving a flavour of object-oriented programming.

Registration and Fee

The course will be held from September 8 to 12 , 2008.

Pre-registration form is available here.

The registration fee for academics is 100 CHF.
The registration fee for industry participant is 150 CHF.


The schedule will be available here.

Location, housing and transportation

See Organisation page.