Master’s Degrees in Bioinformatics in Switzerland:

Past, present and near future

Patricia M. Palagi

Swiss Institute of Bioinformatics

From Oct. 1999 – until Oct. 2004

DEA (undergraduate course) in Bioinformatics organised by the Swiss Institute of Bioinformatics (SIB) and the Universities of Geneva and Lausanne (3 Departments);

Eligibility: students with a degree in biology, medicine, biochemistry, pharmacy or computer sciences.

One year course, 8 modules, 784 hours

Practical training 2-3 months

77 students registered in 5 years, 52 students have finished their degrees so far.

October 2004: end of the last edition!

Programme (1)

Module 1: Introduction to bioinformatics (72 hrs theory + 40 hrs exercises)– Genomics, transcriptomics, proteomics and their bioinformatics

applications

Module 2: Filling the gaps– a) Biochemistry and biology for computer scientists– b) Algorithms, data structures and programming with C++ for

the others (56 + 112 h)Module 3: Databases for life sciences (27 + 24 h)– Large overview of databases contents– SQL, mySQL, Corba, data mining, etc.

Module 4: Probability and statistics (60 + 40 h)

Programme (2)

Module 5: Macromolecular sequence analysis (56 + 24 h)– Sequence similarities, sequence alignments, patterns, profiles, Hidden Markov models, protein functions – Genetic algorithms, neural networks, and other complex adaptive systems

Module 6: Three-dimensional structure analysis (32+8 h)– Secondary structure, protein fold, protein modelling

Module 7: Phylogenetics analysis (44 + 28 h)– Principles and numerical methods in phylogenetics

Module 8: Genomics, transcriptomics et proteomics (56 + 28 h)

– ESTs, gene prediction, genome annotation, SAGE, DNA chips (quantitation, statistics), 2D gel analysis, image analysis, protein identification with mass spectrometry

Bottleneck

Heterogeneity of the student’s background– No experience with programming– Lacking knowledge of statistics

Difficult choice of the programming language (C++, Perl, Java)

Contents versus Available Time

And recently the Bologna agreement

From Oct 2004 – Masters will have to be Bologna* compatible in CH

In general in Switzerland, the Bioinformatics will be inserted in the graduation programs:

In Lausanne- one module in the BSc and one module in the MSc (both in Biology, University of Lausanne) and one module in MSc in Computer Sciences (EPFL)In Basel- one module in the MSc in Computer SciencesIn Geneva, there will be one Master’s in Proteomics and Bioinformatics (to train super-users of Bioinformatics)

www.mpb.unige.ch

SIB will create a PhD school in Bioinformatics from 2005 (EMBL PhD school like).

*Bologna: BSc 3 years + MSc 1½ or 2 years + PhD