1. Master’s Degrees in Bioinformatics in Switzerland: Past, present and near future Patricia M. Palagi Swiss Institute of Bioinformatics

2. 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!

3. 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)

4. 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

5. 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

6. 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 Sciences In 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