Bioinformatics for Cell Biologists

Duration: March 15 - March 19, 2010.

Location: The course venue is CMB (Department of Cell and molecular Biology), room D224, von Eulers väg 3. The computer practicals take place in the Computer hall Space at the Berzeliuslaboratoriet (same building as the KI library, the KI bookstore and the Jöns Jacob Restaurant).

Content: The course provides essential, practical knowledge about computational methods in biology with focus on developmental biology. After completion of the course, students should be able to utilize basic bioinformatics resources and tools. Students should also be able to apply and integrate current, advanced computational biology methods in their research and to make better use of publicly available genome-wide experimental data sets.

Format: The course commences by introducing important sources of public database and analysis tool resources such as sequence analysis methods that have the most wide spread usage in biology. Common sequence analysis tools are described and used in practice to highlight their advantages and limitations. Practical work and discussions bridge sequence analysis to cellular function. The course includes lectures on current advanced topics that will reflect the leading edge of research and cover knowledge integration and essential systems biology. Integration into practice is emphasized by a project involving the use of the bioinformatics resources covered in the course.

Examination: All lectures and exercises are compulsory. In case of absence, lectures can be compensated by a literature assignment and written report. The exam consists of project presentations by the course students using the DBRM wiki platform.

Welcome!

Rickard Sandberg
Assistant Prof, CMB

Monday, March 15
09.00 - 11.00  Introduction to course and Bioinformatics (L1) [pdf]
D224           Helena Storvall 


12.00 - 17.00  Core databases for bioinformatics (C1) [pdf]
Space          Erşen Kavak, Helena Storvall, Daniel Ramsköld


Tuesday, March 16 
09.00 - 09.45  Alignments (L2) [pdf]
D224           Daniel Ramsköld

10.00 - 10.45  Phylogenetics (L3) [pdf]
D224           Prof. Bengt Persson, CMB and LIU

11.00 - 11.45  Protein Sequence Bioinformatics (L4) [pdf]
D224           Prof. Bengt Persson, CMB and LIU

13.00 - 17.00  Computer Excercise 1: Alignments, Genomes and Browsers (C2) [links]
Space          Rickard Sandberg


Wednesday, March 17 
09.00 - 12.00  Computer Exercise 2: Phylogenetics and Proteins (C3)
Space          Rickard Sandberg

13.30 - 15.00  Invited Speaker 1: 
D224           Transcriptome and translational regulation
               Dr. Ola Larsson, McGill University

15.30 - 17.00  Gene Expression bioinformatics (L5) [pdf]
D224           Rickard Sandberg


Thursday, March 18 
09.00 - 12.00  Computer Exercise 3: Tools for Next-Gen Sequencing, Galaxy (C4)
Space          Rickard Sandberg

13.00 - 14.30  Bioinformatics of microRNA target predictions (L6) [pdf]
D224           Rickard Sandberg

15.00 - 16.30  Statistical issues with genome-wide experiments (L7) [pdf]
D224           Yudi Pawitan, Dept of Medical Epidemiology and Biostatistics               

Friday, March 19 
09.00 - 11.00  Project work 

12.00 - 15.00  Project presentations (20 min per group) 

15.00 - 16.00  Wrap-up and course evaluation 
               Rickard Sandberg