Bioinformatics for Cell Biologists

Duration: May 21-25 2012.
Location: The course venue is CMB (Department of Cell and molecular Biology), room A216, Berzelius vag 35. The computer practicals take place in the Computer hall Enter 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

Schedule:

Monday, May 21
09.00 - 11.00  Introduction to course and Bioinformatics (L1) 
A216           Assist Prof. Rickard Sandberg

11.00 - 17.00  Computer exercise: Core databases for bioinformatics (C1) [pdf]
Enter          Rickard Sandberg and Dr. Ersen Kavak
               optional reading: pdf


Tuesday, May 22 
09.00 - 09.45  Alignments (L2) 
D224           Daniel Ramsköld

10.00 - 11.00  Phylogeny
D224           Associate Professor Lars Arvestad, NADA KTH

11.00 - 12.00  Protein bioinformatics
               Dr. Åsa Björklund

13.00 - 17.00  Computer Exercise: Alignments, Genomes and Browsers (C2) [links]
Enter          Dr. Åsa Björklund and Daniel Ramsköld
               Tutorial1,  Galaxy101, GalaxyLab2


Wednesday, May 23 
09.00 - 10.00  Microarray analyses
A216           Assistant Professor Ola Larsson, CCK, KI
               pdfs:
 
10.00 - 11.00  Next-generation sequencing bioinformatics
A216           Rickard Sandberg

11.00 - 12.00  RNA-Seq analyses
A216           Rickard Sandberg

13.00 - 17.00  Computer Exercise: RNA-Seq and microarrays 
Enter          Ola Larsson and Rickard Sandberg


Thursday, May 24 
09.00 - 10.00  Bioinformatics of small non-coding RNAs
A216           Dr. Helena Persson, Novum, KI

10.00 - 11. 00 Statistics for genomic studies
A216           Rickard Sandberg

11.00 - 12.00  ChIP-Seq analyses
A216           Dr. Mikael Huss, SciLife Lab, KI

13.00 - 17.00  Computer Exercise: ChIP-Seq analyses and repositories for genomic data
Enter          Rickard Sandberg and Mikael Huss


Friday, May 25 
09.00 - 10.15  Preparation time for individual presentations
A216

10.15 - 11.15  Transcriptome reconstructions
A216           Assistant Professor, Manfred Grabherr, SciLife lab, Uppsala 

11.15 - 12.15  Synteny in comparative genomics 
A216           Assistant Professor, Manfred Grabherr, SciLife lab, Uppsal

13.00 - 15.30  Examination presentations
A216

15.30 - 16.00  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