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Course Overview 2007

June 4 to 22, 2007
Lectures and exercises will take place at CBS, Technical University of Denmark, building 210, room 118 in Lyngby.

Daily schedule:
Lectures will be from 9.30 - 12.00
Lunch from 12.00 - 13.00 and
Exercises from 13.00 - 16.00






EVALUATION FORMS


O Monday, June 4

9.30-10.30
Introduction to the course and a general overview
Carsten Friis, CBS
10.30-11.00
Coffee Break
11.00-12.00
Gene Discovery and Genome Browsing
Background text
Thomas Nordahl Petersen, CBS
12.00-13.00
Lunch Break
13.00-16.00
Exercises: Genome Browsing
Thomas Nordahl Petersen


O Tuesday, June 5

Grundlovsdag: This is a national holiday


O Wednesday, June 6

9.30-10.30
Biological Network Analysis
Background text
Chris Workman, CBS
10.30-11.00
Coffee Break
11.00-12.00
Eukaryotic gene prediction
Background text
Kai Wang, CBS
12.00-13.00
Lunch Break
13.00-16.00
Exercises: Gene Prediction
Answer Form
Kai Wang


O Thursday, June 7

9.30-10.30
A systems biology approach to the dissection of patho-biologies in COPD
Ib Groth Clausen, Astra Zeneca AB, Sverige
10.30-11.00
Coffee Break
11.00-12.00
microRNA
Background text
Thomas Litman, BINF, KU + Exiqon
12.00-13.00
Lunch Break
13.00-16.00
Exercise: microRNA
Thomas Litman


O Friday, June 8

9.30-10.30
Affymetrix case study VM-story
Background text
Jesper Jørgensen, NsGene
10.30-11.00
Coffee Break
11.00-12.00
Literature mining & systems biology
Background text
Lars Juhl Jensen, EMBL, Germany
12.00-13.00
Lunch Break
13.00-14.00
Exercises: Literature mining
Lars Juhl Jensen
14.00-14.30
Coffee Break
14.30-16.00
Formation of Project Groups
Carsten Friis


O Monday, June 11

9.30-10.30
Genetics & Gene Discovery
Niels Tommerup, IMBG, KU
10.30-11.00
Coffee Break
11.00-12.00
Disease gene finding
Background text
Kasper Lage Hansen, CBS
12.00-13.00
Lunch Break
13.00-16.00
Exercises: Disease gene finding
Handout 1; Handout 2
Kasper Lage Hansen


O Tuesday, June 12

9.30-10.30
Genes and IPR
Background text
Jens V. Nørgaard, Symphogen A/S
10.30-11.00
Coffee Break
11.00-12.00
Genes and IPR
Background text
Jens V. Nørgaard
12.00-13.00
Lunch Break
13.00-14.00
Navigating the miRNA world in silico and in vitro
Niels Tolstrup, Exiqon
14.00-14.30
Coffee Break
14.30-16.00
On the Speed of Sequencing Genomes
David W Ussery, CBS


O Wednesday, June 13

9.30-10.30
Quantitave PCR
Background text
Claus Hansen, WJC, KU
10.30-11.00
Coffee Break
11.00-12.00
Introduction to Bacterial PanGenomics
Background text
David W Ussery, CBS
12.00-13.00
Lunch Break
13.00-16.00
Exercise: Visualizing genomes
David W Ussery
CBS atlas pages (use these for the exercises)      v3.0 atlas pages (under development)      zoom atlases      NCBI      Exercise Solutions


O Thursday, June 14

9.30-10.30
Motif mining and phosphoproteomics
Background text
Martin Miller, CBS
10.30-11.00
Coffee Break
11.00-12.00
Classification Methods; Machine Learning
Michael Kerner, CBS
12.00-13.00
Lunch Break
13.00-16.00
Exercise: Classification using the WEKA Tool
Michael Kerner


O Friday, June 15

9.30-12.00
Selection of Project Topics and Collection of Information for Project
Poster Specifications; Student Groups; Example Poster


O Monday, June 18 – Wednesday, June 20

PROJECT WORK – including preparation of Poster for Poster Session

10.00-12.00
Office Hours in Classroom


O Thursday, June 21

14:00
Deadline for uploading your poster presentation (Name it Group-X.ppt and upload to this link or mail to )
Deadline for uploading your 2-3 page poster summary (Name it Group-X.doc and upload to this link or mail to )
16.00-???
Poster Session and Party!!


O Friday, June 22

EXAM: Oral Poster Presentations in Plenum
Censor: Ole Lund

9.30-10.00
Presentation by Group 1
10.00-10.30
Presentation by Group 2
10.30-11.00
Coffee Break
11.00-11.30
Presentation by Group 3
11.30-12.00
Presentation by Group 4
12.00-12.30
Presentation by Group 5
12.30-13.00(?)
Summary, Discussion, Evaluation and Goodbye
Carsten Friis