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Course Programme 2007



The course will be held from April 16 - 27, 2007 (incl.)
Please note that due to the limited space, only those registered can participate in the Spring 2007 course.

Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, auditorium 062.

DAILY SCHEDULE:
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 16.30 pm.
Discussion from 16.30 - 17.00 pm.
For the afternoon exercises you are supposed to log on to one of CBS' central servers using the User ID and password forwarded to you in an email.
To avoid overloading any single machine,
users 1 - 25 should log on to 'cell.cbs.dtu.dk';
users 26 - 52 should log on to 'organism.cbs.dtu.dk'
- via ssh.

Beginner's Guide to UNIX
Programs and tools for internet students

EVALUATION FORMS
Please fill out the evaluation forms daily. Your feedback will help us improve the course.


O Monday, April 16


Pair-wise Alignment and Database Searching
Recordings:    Brunak    Nielsen    Exercise intro    During exercise    Exercise summary
9.00-9.45
Introduction to bioinformatics and systems biology
Søren Brunak
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
Henrik Nielsen Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: searching databases of nucleotide and amino acid sequences
Henrik Nielsen
16.30-17.00
Discussion

O Tuesday, April 17

Hidden Markov Models and Gene Finding
Recordings:    Nielsen_1    Blom_1    Blom_2    Exercise intro, MN    During exercise, MN    Exercise summary, MN    Exercise intro, NB    During exercise, NB    Exercise summary, NB
9.00-10.00
Finding sequence motifs: consensus sequences, weight matrices, information content,
sequence logos, and Hidden Markov Models

Morten Nielsen
10.00-10.30
Coffee Break
10.30-12.00
Eukaryotic gene finding
Nikolaj Blom   Handout (PDF) ONLINE PARTICIPANTS: PLEASE PRINT BEFORE LECTURE
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Hidden Markov model and weight matrix construction
Morten Nielsen
Gene finding in eukaryotes
Exercise evaluation form (*doc)
Nikolaj Blom
16.30-17.00
Discussion

O Wednesday, April 18

Datadriven Prediction
Recordings:    Brunak_1    Brunak_2    Brunak_3    During exercises    Discussion
9.00-10.00
Datadriven prediction methods and neural networks
Søren Brunak
10.00-10.30
Coffee Break
10.30-11.30
Applications: learning from evolution to predict protein structure
Søren Brunak
11.30-12.00
Application: prediction of post-translational modifications and protein function
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
16.30-17.00
Discussion

O Thursday, April 19

Multiple Alignment and Phylogeny
Recordings:    Blom    Gorm_1    Gorm_2    Exercise intro    During exercise    Exercise summary
9.00-9.45
Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome
Nikolaj Blom
9.45-10.15
Coffee Break
10.15-12.00
Multiple alignment and phylogenetic reconstruction
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 Results form
16.30-17.00
Discussion

O Friday, April 20

Immunology and Phylogeny
Recordings:     Lundegaard     Gorm     Exercise_intro     During exercise + summary
9.00-9.45
Immunological bioinformatics
Claus Lundegaard
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny
Anders Gorm Pedersen
Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Maximum likelihood phylogeny
Anders Gorm Pedersen Results form
16.30-17.00
Discussion

O Monday, April 23

Fold Recognition
Recordings:     Thomas Blicher     Pernille     Morten     Intro to exercise     Exercise summary
9.00-9.45
Protein Structure
Thomas Blicher
9.45-10.15
Coffee Break
10.15-11.00
Protein Secondary Structure Prediction
Pernille Andersen
11.15-12.00
Fold Recognition
Morten Nielsen
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Claus Lundegaard and Morten Nielsen
16.30-17.00
Discussion

O Tuesday, April 24

Protein Modelling and Drug Discovery
Recordings:     Thomas Nordahl     Anne Marie     Thomas Blicher     Intro to exercise     During exercise     Exercise summary
9.00-09.45
Gene Discovery by use of MySQL
Thomas Nordahl Petersen  
09.45-10.15
Coffee Break
10.15-11.00
Computational decision support for drug design. Profilling of small molecule compound libraries
Anne Marie Munk Jørgensen  
11.15-12.00
Homology modeling and model evaluation
Thomas Blicher  
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology modeling
Thomas N. Petersen, Thomas Blicher

O Wednesday, April 25

Systems biology
Recordings:     Chris Workman     Thomas Skøt     Case story     Exercise summary
9.00-09.45
Introduction to systems biology
09.45-10.15
Coffee Break
10.15-11.00
Biological network analyses
11.00-11.15
Coffee break
11.15-12.00
Case story: DNA damage response
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Building networks, data integration and network analyses
16.30-17.00
Discussion

O Thursday, April 26

Gene Expression and DNA array technology
Recordings:     H. Bjørn 1     H. Bjørn 2     Case story (H. Bjørn)     Discussion
9.00-9.45
Introduction to DNA microarray technology
Hanne Jarmer
9.45-10.15
Coffee Break
10.15-12.00
Data analysis: pre-processing and statistics,     Case story (slides not available)
H. Bjørn Nielsen
12.00-13.00
Lunch Break
13.00-15.30
Discussion/exercise: questions answers
H. Bjørn Nielsen

O Friday, April 27

Comparative genomics
Recordings:    None yet
9.00-9.45
Introduction to Comparative Genomics
David Ussery
9.45-10.15
Coffee Break
10.15-11.00
Methods to Compare Microbial Genomes
David Ussery
11.00-11.15
Break
11.15-12.00
Comparative PanGenomics
David Ussery
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Comparative Genomics using Web Services
David Ussery and Peter Hallin
16.30-17.00
Discussion


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