Sandberg Lab

Ludwig Institute for Cancer Research & Department of Cell and Molecular Biology, Karolinska Institutet

Bioinformatics for Cell Biologists

Duration: May 9-13 2011.
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.


Rickard Sandberg


Monday, May 9
09.00 - 10.30  Introduction to course and Bioinformatics (L1) 
D224           Assist Prof. Rickard Sandberg

12.00 - 17.00  Computer exercise: Core databases for bioinformatics (C1) [pdf]
Space          Dr. Erşen Kavak, Helena Storvall, Rickard Sandberg
               optional reading: pdf

Tuesday, May 10 
09.00 - 09.45  Alignments (L2) [pdf]
D224           Daniel Ramsköld

10.00 - 12.00  Genome Assemblies and Bioinformatics (L3)
D224           Dr. Erik Arner, RIKEN OMICS Center, Yokohama, Japan

13.00 - 17.00  Computer Exercise 1: Alignments, Genomes and Browsers (C2) [links]
Space          Dr. Erik Arner (and Carsten or Rickard), RIKEN OMICS Center, Yokohama, Japan
               Tutorial1,  Galaxy101, GalaxyLab2

Wednesday, May 11 
09.00 - 11.00  Gene expression and next-generation sequencing Bioinformatics
D224           Rickard Sandberg
               pdfs: pdf, pdf, pdf

11.00 - 12.00  ChIP-Seq Bioinformatics
D224           Mikael Huss, Science for Life Lab, KI/KTH/SU

13.00 - 17.00  Computer Exercise: RNA-Seq and ChIP-Seq [doc]
Space          Daniel Ramskold and Helena Storvall

Thursday, May 12 
09.00 - 11.00  Phylogenetics and Protein Bioinformatics
D224           Prof Bengt Persson, KI and LiU
               pdfs: pdf

11.00 - 12. 00 Microarray data analyses
D224           Dr. Ola Larsson, CCK, KI
               pdfs: pdf, pdf, pdf 

13.00 - 17.00  Computer Exercise: Phylogenetics and Microarrays [phylogenetics, microarray]
Space          Daniel Ramskold and Ola Larsson

Friday, May 13 
09.00 - 13.30  SciLifeLab and RIKEN Yokohama Joint Seminar, at Nobels forum [pdf] 
14.30 - 15.30 Wrap-up and course evaluation Rickard Sandberg

Additional Course Links:

Links to a large number of introductions to computational biology techniques and questions - recommended
UCSC Genome Browser
DBRM course homepage
Wiki for project work. Works in Internet Explorer or Safari.
Integrated Genomics Viewer

Additional (optional) labs:
GalaxyExcersice_regulation.pdf, GalaxyExcersice_transcripts_and_splicing.pdf, TF_prediction.pdf

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