Unix & Perl for biomedical researchers 2006


Using the web interface 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 very basic knowledge of Unix command-line and PERL scripting abilities to analyse large amounts of data by automating recurring tasks or by grouping several tasks into one command.
This course is organised for biomedical researchers and no particular programming knowledge is required.

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. Only basic Unix skills is recommended.


Course objectives

- ensuring familiarity with basic computer concepts and their everyday use in a biological laboratory setting.
- teaching them basic UNIX commands and the UNIX file structure.
- 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 was held from October 9 to October 13, 2006.

The registration opens on April 1st.

The registration fee for academics is 100 CHF.


The schedule will be available here.

Location, housing and transportation

See Organisation page.