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Course Programme 2010
The course will be held from May 31 - June 11, 2010 (incl.)
Please note that due to the limited space, only those registered can participate
in the Spring 2010 course.
Lectures and exercises will take place at the
Center for Biological Sequence Analysis, DTU, building 208, auditorium 062 (in the basement).
DAILY SCHEDULE:
09:00 - 12:00 Lectures
12:00 - 13:00 Lunch
13:00 - 16:30 (approximately): Exercises
16:30 - 17:00 (approximately): Discussion
For some of the afternoon exercises you are supposed to log on to one of CBS' central servers using the User ID and
password that will be forwarded to you in an email.
Please note: lecturers will be working on powerpoints and handouts until the last minute, so changes
may occur!
Setting up your own computer for the course
Beginner's
Guide to UNIX
Another beginner's guide to UNIX
Monday, May 2
Pair-wise Alignment and Database Searching
- 9.00-9.45
-
Introduction to Bioinformatics?
[PPT]
[PDF]
Anders Gorm Pedersen
- 9.45-10.15
- Coffee Break
- 10.15-12.00
- Pairwise sequence alignment and database searching: global and local alignments, substitution matrices, gap penalties, statistical
significance
Slides:
[PPT]
[PDF]
Handout: [PDF]
Anders Gorm Pedersen
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
searching databases of nucleotide and amino acid
sequences
Anders Gorm Pedersen
- 16.30-17.00
- Discussion
Tuesday, May 3
Multiple Alignment and Phylogeny
- 9.00-9.45
- Multiple alignment and phylogenetic reconstruction
[PPT]
[PDF]
Anders Gorm Pedersen
- 9.45-10.15
- Coffee Break
- 10.15-12.00
- Multiple alignment and phylogenetic reconstruction (continued)
Anders Gorm Pedersen
Handout [PDF]
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
multiple alignments,
construction of phylogenetic trees
Anders Gorm Pedersen
- 16.30-17.00
- Discussion
Wednesday, May 4
Maximum Likelihood Phylogeny
- 9.00-9.45
- Assorted issues in multiple alignment and phylogeny
[PPT]
[PDF]
Anders Gorm Pedersen
- 9.45-10.15
- Coffee Break
- 10.15-12.00
- Maximum likelihood phylogeny
[PPT]
[PDF]
Anders Gorm Pedersen
Handout [PDF]
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Maximum likelihood phylogeny
Anders Gorm Pedersen
- 16.30-17.00
- Discussion
Thursday, May 5
Second Generation Sequencing, Genomics, Functional Variation
- 9.00-10.30
- Lecture: Cautionary Tales of Next-generation Sequencing (Dave Ussery) (incl. 20-30min break)
Dave Ussery
[PDF] - 9.45-10.15
- Coffee Break
- 10.30-11.00
- Exercise: NGEN seq. reference_mapping.doc: (2-page document printed on A4.)
Dave Ussery, Ramneek Gupta
- 11.00-12.00
- Next Generation Sequencing Technology: HiSeq
Illumina
[PDF]
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Case story: The ancient genome sequencing project
Ramneek Gupta
- Exercise:
Genotype to Phenotype
AssemblyPoster.xls:
(one page, preferably print on A3 in colour, but A4 should work too. A pair of scissors is needed later)
Ramneek Gupta, Thomas Sicheritz-Ponten
- 16.30-17.00
- Discussion
Friday, May 6
Protein Modelling and Drug Discovery
- 9.00-09.45
- Gene Discovery by use of MySQL
Thomas Nordahl Petersen
- 09.45-10.15
- Coffee Break
- 10.15-11.00
- Homology modeling and model evaluation
Thomas Blicher
- 11.15-12.00
- Drug design
Irene Kouskoumvekaki
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Homology modeling
,
Drug design
Thomas N. Petersen, Thomas Blicher & Irene Kouskoumvekaki
Monday, May 9
Hidden Markov Models, Immunological Bioinformatics
- 9.00-10.00
- Introduction to the immune system
Ole Lund
- 10.00-10.30
- Coffee Break
- 10.30-11.15
- Finding sequence motifs: consensus sequences,
weight matrices, information content,
sequence logos,
and Hidden Markov Models
- Handout for the lecture:
How to estimate pseudo counts (online students please print out before lecture!)
Morten Nielsen
-
How to estimate pseudo counts (Answers)
- 11.15-12.00
- MHC binding and MHC polymorphism
Morten Nielsen
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Weight matrix construction and sequence logos
Morten Nielsen
Development of vaccines against HCV
Morten Nielsen, and Ole Lund
- 16.30-17.00
- Discussion
Tuesday, May 10
Analysis of gene-expression data on a genome-wide scale
- 9.00-9:45
-
Introduction to the DNA microarray technology
Hanne Jarmer
- 9.45-10.15
- Coffee Break
- 10.15-11.00
-
Data analysis I: Preprocessing and statistics
Hanne Jarmer
- 11.15-12.00
-
Data analysis II: Clustering and dimension reduction
Hanne Jarmer
- 12.00-13.00
- Lunch Break
- 13.00-14.45
-
Discussion/exercise I: The technology, preprocessing and statistics
->
answers
Hanne Jarmer
- 14:45-15:00
- Break
- 15.00-16.30
-
Discussion/exercise II: Clustering and dimension reduction
->
answers
Hanne Jarmer
Wednesday, May 11
Datadriven Prediction
- 9.00-10.00
- Neural networks for biological sequence analysis
Søren Brunak
- 10.00-10.30
- Coffee Break
- 10.30-11.30
- Neural network prediction systems - signal peptides and gene structure
Søren Brunak
- 11.30-12.00
- Neural networks for prediction of diverse, systems biology related categories
Søren Brunak
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
signal peptide prediction,
neural network training,
performance measures and evaluation of prediction quality
Søren Brunak and Henrik Nielsen
- 16.30-17.00
- Discussion
Thursday, May 12
Systems biology
Recordings:
Workman: Session 1
Workman: survey + session 2
Workman: Session 3
Workman: session 3 continued
Workman: von mering+cyctoscape
Workman:brief intro to exercise
Workman:exercise continued
Workman:session 4
- 9:00-10:00
- Overview, Survey, Motivation for Systems Biology
Lecture slides,
Click here to take survey
- 10:00-10:20
- Coffee Break
- 10:20-10:50
-
Interaction networks: data and properties
- 10:50-11:10
- Discussion: Pluses and minuses of HTP interaction data sets
Questions,
von Mering et al.,
Slides
- 11:10-11:20
- Break
- 11:20-12:00
- Exercise:
Protein interaction networks and network properties
,
RUAL.subset.sif ,
RUAL.subset.names.tab
- 12:00-13:00
- Lunch Break
- 13:00-13:50
-
Transcription factor binding location analysis (chIP-chip), Active modules approach
- 13:50-14:00
- Break
- 14:00-14:40
-
Functional genomics and inferring regulatory pathways
- 14:40-15:00
- Conclusions and wrap-up
Friday, May 13
Fold Recognition
- 9.00-9.45
- Protein Structure
Thomas Blicher
- 9.45-10.15
- Coffee Break
- 10.15-11.00
-
Protein Local Structure Prediction
Morten Nielsen
- 11.15-12.00
- Fold Recognition
- Handout exercise
Morten Nielsen
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Fold recognition using web servers
Morten Nielsen
- 16.30-17.00
- Discussion
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This file was last modified Thursday 14th 2011f April 2011 05:36:43 GMT |
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