Introduction to Bioinformatics: A course for MSc and BSc students of the University of Bern

(There is a separate course for PhD students each November, for 2010 dates are 21-25 november 2010. Every day 9:30 AM to 17:00 PM, Please contact Dr. AV Pandey (amit@pandeylab.org or Dr. Marlene Wolf, Graduate School Coordianator marlene.wolf@tki.unibe.ch)

 

Dates: Feb 25, March 4, 18, 25 April 1, 15, 22, 29 May 6, 20, 27 2010 (Thursday)

Time : 14:15-18:00 PM

Place: F123/B-181, UniTobler, Lerchenweg 36, Bern

Lecture in Room   F-123                             :   14:15-15:45

Practical in Room B-181                              :   16:00-18:00

Registration: https://ilias.unibe.ch/goto_ilias3_unibe_crs_117607.html

(Practical part of the course will be divided into two groups of 25 students each on different days)  

Course content

 Each topic will be covered in 1 or 2 lectures of 45 min (F-123 UniTobler) followed by 2 hours of practical hands on training on computer terminals at Unitobler PC/Mac course room (B-181 UniTobler). Total number of students per semester is limited to 50-55 and students for whom this course is required will have priority (BSc 6th semester in Cell Biology, BSc 6th semester in Biochemistry).

 An exam for students requiring credit points will be conducted after the course. Students will be given short projects that they will have to complete and submit for evaluation. An oral exam of 10 min duration will be conducted to go through the project and award final grades. Attendance and mini projects during the course will also be considered when awarding grades.

 

  1. Bioinformatics tools & major portals for searching databases (EBI, NCBI, UCSC genome browser).

  2. DNA & Protein databases, Genome databases, SNP (mutations/polymorphisms).

  3. Literature, metabolomics, KEGG, OMIM, proteomics, structure, expression databases.

  4. Biological pathways, interaction databases.

  5. DNA and Protein sequence analysis

  6. Similarity searches (BLAST, PhiBLAST …)

  7. Sequence alignments (Two sequence, multiple sequence) and editing.

  8. Bioinformatics servers for posttranslational modifications, sub-cellular localization, profile and family searches.

  9. Secondary structure analysis of proteins

  10. Brief introduction to 3D structure visualization and analysis of proteins.

  11. Practical tools for primer design (PCR, RNAi/shRNA), sequence alignment for publications, NIH Image for gel scan analysis.

Books: Most of the course content will use online tools at European Bioinformatics Institute web servers. Following books may be consulted for coverage of course content. Books are available at Studentische Buchgenossenschaft (http://www.bugeno-unibe.ch) or Stauffacher.ch/Amazon.de

Bioinformatics for Dummies 2nd Edition 2007 (ISBN 0-470-08985-7) by Jean-Michel Claverie & Cedric Notredame. This will cover most of the course content.

Bioinformatics: A practical guide to the analysis of genes and proteins. 3rd Edition 2005 (ISBN 0-471-47878-4) Ed. Andreas D Baxevanis & B. F. Francis Ouellette.

 Contact: Dr. Amit V Pandey, Pediatric Endocrinology, Diabetology & Metabolism, Department of Clinical Research, Tiefenaustrasse 120c, 3004 Bern. Tel: 031 308 8044. Email: amit@pandeylab.org