Sandberg Lab

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

Bioinformatics for Cell Biologists

Duration: May 19-23 2014.
Location: The course venue is CMB (Department of Cell and molecular Biology), room A216, Berzelius vag 35.

Bring your own laptop for the computer labs

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

Preliminary Schedule 2014:

Monday, May 19
09.00 - 11.00  Introduction to course and Bioinformatics (L1) 
A216           Assoc Prof. Rickard Sandberg

11.00 - 17.00  Computer exercise: Genome browsing and genome-wide bioinformatics with Galaxy (C1) 
A216           Rickard Sandberg
               optional reading: pdf

Tuesday, May 20 
09.00 - 09.45  Alignment (L2) [pdf]
	       Daniel Ramskold

10.00 - 11.00  Phylogeny [pdf]
A216           Associate Professor Lars Arvestad, NADA KTH

11.00 - 12.00  Protein bioinformatics [pdf]
A216           Dr. Asa Bjorklund

13.00 - 17.00  Computer Exercise: Alignments and protein bioinformatics (C2) [exercises, optional phylogeny exercise] 
A216           Dr. Asa Björklund and Daniel Ramsköld

Wednesday, May 21 
09.00 - 10.00  Gene expression analyses (RNA-seq and microarrays) 
A216           Rickard Sandberg
10.00 - 11.00  Introduction to Bioinformatics resources in Sweden
A216           Dr. Asa Bjorklund, WABI

11.00 - 12.00  Next-generation sequencing bioinformatics [pdf]
A216           Helena Storvall

13.00 - 17.00  Computer Exercise: RNA-Seq 
A216           Daniel Edsgard and Rickard Sandberg

Thursday, May 22 
09.00 - 10.00  ChIP-seq analyses
A216           Dr. Jakub Westholm , WABI, SciLifeLab

10.00 - 11.00  Statistics for genomic studies [pdf]
A216           Rickard Sandberg
               optional reading: pdf

11.00 - 12.00  GWAS studies
A216	       Dr. Daniel Edsgard

13.00 - 17.00  Computer Exercise: ChIP-Seq analyses and repositories for genomic data [link to exercise, data for optional IGV browsing]
A216           Daniel Ramskold and Daniel Hagey

Friday, May 23 
09.00 - 10.00  Preparation time for individual presentations

10.00 - 12.00  Examination, individual presentations

13.00 - 14.00  Examination, individual  presentations

14.00 - 14.30  Course evaluation and wrap-up
A216           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

Additional custom STARR-Seq data: bamfile and indexfile,
and filtered for only Chr1: bamfile and indexfile.

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