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Course Programme 2008
The course will be held from May 19 - 30, 2008 (incl.)
Please note that due to the limited space, only those registered can participate
in the Spring 2008 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:
09:00 - 12:00 Lectures
12:00 - 13:00 Lunch
13:00 - 16:30 (approximately): Exercises
16:30 - 17:00 (approximately): Discussion
For 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
Monday, May 19
Pair-wise Alignment and Database Searching
Recordings:
Henrik Nielsen 1st lecture
Henrik Nielsen, 2nd. Lecture
Exercise introduction
Exercise introduction, part 2
During exercise
Exercise summary
- 9.00-9.45
-
What is Bioinformatics?
[PPT]
[PDF]
Henrik Nielsen
- 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]
Henrik Nielsen
- 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
Evaluation form, May 19
Tuesday, May 20
Multiple Alignment and Phylogeny
Recordings:
Anders, 1st lecture
Anders, 2nd. Lecture
Anders, 2nd lecture, after handout
Exercise introduction
Exercise summary
- 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
Evaluation form, May 20
Wednesday, May 21
Maximum Likelihood Phylogeny
Recordings:
Anders, 1st lecture
Anders, 2nd. Lecture
Exercise introduction
Exercise summary
- 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]
Handout results: [PDF]
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Maximum likelihood phylogeny
Anders Gorm Pedersen
- 16.30-17.00
- Discussion
Evaluation form, May 21
Thursday, May 22
Hidden Markov Models and Gene Finding
Recordings:
Morten, HMM
Claus, gene finding
Gene finding exercise intro
Gene finding exercise
T cell epitope exercise intro
T cell epitope exercise
T cell epitope exercise, summary
- 9.00-10.00
- 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
- 10.00-10.30
- Coffee Break
- 10.30-11.15
- Prokaryotic gene finding
Claus Lundegaard
- 11.15-12.00
- Eukaryotic gene finding
Claus Lundegaard
Handout (PDF)
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Gene finding in
eukaryotes
Claus Lundegaard
Hidden Markov model and weight matrix construction
Morten Nielsen
- 16.30-17.00
- Discussion
Evaluation form, May 22
Friday, May 23
Gene Expression and DNA array technology
Recordings:
Hanne, micro array intro
Bjørn, analysis
Bjørn, case story
Exercises intro
Exercises, session 2
Exercises, last session
- 9.00-9.45
- Introduction to DNA microarray technology
Hanne Jarmer
- 9.45-10.15
- Coffee Break
- 10.15-12.00cd
- Data analysis: pre-processing and statistics,
Case story: FARO
Nielsen et al., 2007
H. Bjørn Nielsen
- 12.00-13.00
- Lunch Break
- 13.00-15.30
- Discussion/exercise: questions
answers
H. Bjørn Nielsen
Evaluation form, May 23
Monday, May 26
Fold Recognition
Recordings:
Thomas, protein structure
Morten, secondary structure
Morten, fold recognition
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
Morten Nielsen
- 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
Evaluation form, May 26
Tuesday, May 27
Protein Modelling and Drug Discovery
Recordings:
Thomas Nordahl, partial recording
Thomas Blicher
Olivier Taboureau
Thomas N, Exercise-intro
Thomas N, exercise summary
Olivier, exercise intro
Olivier, exercise details
Olivier, 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
- Homology modeling and model evaluation
Thomas Blicher
- 11.15-12.00
- Drug design
Olivier Taboureau
- 12.00-13.00
- Lunch Break
- 13.00-16.30
- Exercises:
Homology modeling
,
Drug design
Thomas N. Petersen, Thomas Blicher & Olivier Taboureau
Evaluation form, May 27
Wednesday, May 28
Datadriven Prediction
Recordings:
Brunak 1
Brunak 2
Brunak 3
Exercise intro
During exercise 1
Exercise 1 summary + exercise 2 intro
During exercise 2
Exercise 2 summary
- 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
Evaluation form, May 28
Thursday, May 29
Systems biology
Recordings:
Chris Workman 1
Chris Workman 2
Chris Workman 3
Chris Workman 4
- 9:00-9:50
- Overview and pre-module survey/quiz, Motivation for Systems Biology
Lecture slides,
Survey/Quiz
- 9:50-10:20
- 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
- 13:00-13:30
-
Transcription factor binding location analysis (chIP-chip), Active modules approach
- 13:30-14:30
- Exercise:
Integrating gene expression data with protein interaction data (Active Modules)
- 14:30-14:45
- Break
- 14:45-15:15
-
Functional genomics and inferring regulatory pathways
- 15:15-15:45
- Finish Cytoscape exercises 1 and 2, explore more advanced usage
- 15:45-16:00
- Conclusions and wrap-up
Evaluation form, May 29
Friday, May 30
Immunological Bioinformatics
Recordings:
Claus, 1st lecture
Pernille, 2nd lecture
Morten, 3rd lecture
Claus, 4th lecture
B-cell exercise, intro
B-cell exercise summary
HCV vaccine exercise intro
HCV vaccine exercise summary
- 9.00-09.30
- Introduction to the immune system
Claus Lundegaard
- 9.30-10.00
- Antibody responses to linear and conformational epitopes
Pernille Andersen
- 10.00-10.30
- Coffee Break
- 10.30-11.15
- MHC binding and MHC polymorphism
Morten Nielsen
- 11.15-12.00
- Processing, prediction integration, and rational epitope selection.
Claus Lundegaard
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Exercises: Predictions of B cell epitopes in proteins
Pernille Andersen
- 14.00-14.30
- Break
- 14.30-16.30
- Exercises: Development of vaccines against HCV
Morten Nielsen
- 16.30-17.00
- Discussion
Evaluation form, May 30
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This file was last modified Tuesday 4th 2013f June 2013 11:49:23 GMT |
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