Program 2019
REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES
Lectures and exercises will take place at the Section for Bioinformatics at the Technical University of Denmark, Building 208, Room 062 in Lyngby (map).
The courses has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on Thursday 27th of June.
This term we will be using Piazza for class discussion. The system is highly catered to getting you help fast and efficiently from classmates, the TA, and myself. Rather than emailing questions to the teaching staff, I encourage you to post your questions on Piazza here
Course Program - June 2019
Thursday, June 6
Introduction - Next Generation Sequencing
- 9.00-9.30
- Introduction to course & Pre-test (Lecture slides) (Pre-test)
- Gisle Vestergaard
- 9.30-10.00
- Introduction to NGS (Lecture slides)
- Gisle Vestergaard
- 10.00-10.45
- 2nd and 3rd generation NGS Technologies (Lecture slides)
- Gisle Vestergaard
- 10.45-11.00
- Break
- 11.00-12.00
- Tech talk group formation and group work (Lecture slides) (Student Groups)
- Gisle Vestergaard
- 12.00-13.00
- Lunch Break
- 13.00-13.30
- Exercise: Logging on to our Computerome cloud (Logging on to Cloud system)
- Gisle Vestergaard, Katrine Højholt
- 13.30-14.15
- Introduction to UNIX (Lecture slides) (Exercise) (Unix Notes)
- Peter Wad Sackett, Gisle Vestergaard
- 14.15-14.30
- Break
- 14.30-15.30
- Introduction to UNIX (Lecture slides) (Exercise) (Unix Notes)
- Peter Wad Sackett, Gisle Vestergaard, Katrine Højholt
- 15.30-16.00
- First look at data (First look exercise)
- Gisle Vestergaard, Katrine Højholt
Friday, June 7
Data pre-processing & Genomic Epidemiology
- 9.00-10.45
- Data basics (Lecture slides) (Data basics exercise) (Data basics solution)
- Gisle Vestergaard, Katrine Højholt
- 10.45-11.00
- Break
- 11.00-12.00
- Data pre-processing (Lecture slides) (Data Preprocess exercise) (Data Preprocess solution)
- Katrine Højholt
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Exercise: Genomic Epidemiology (Genomic epidemiology exercise) (Genomic epidemiology solution)
- Gisle Vestergaard, Katrine Højholt
- 14.00-16.00
- Case story: Genomic Epidemiology (Lecture)
- Pimlapas Leekitecharoenphon (Shinny)
Monday, June 10
Whit Monday - No teaching!
Tuesday, June 11
Alignment & Genotyping
- 9.00-9.45
- Alignment (Lecture slides)
- Gisle Vestergaard
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: Alignment (Alignment exercise) (Alignment solution)
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
- 12.00-13.00
- Lunch Break
- 13.00-13.25
- Functional Human Variation
- Jose Izarzugaza (Txema) (Lecture slides)
- 13.25-14.00
- Alignment postprocessing & variant calling (Lecture slides)
- Gisle Vestergaard
- 14.00-14.15
- Break
- 14.15-16.00
- Exercise: Postprocessing & variant calling (Postprocess exercise) (Postprocess solution) (SNP calling exercise) (SNP calling solution)
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
Wednesday, June 12
de novo assembly & Metagenomics
- 9.00-9.45
- Lecture: de novo assembly (Lecture slides) (Handout)
- Gisle Vestergaard
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: de novo assembly (denovo exercise) (denovo solution)
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
- 12.00-13.00
- Lunch Break
- 13.00-13.45
- Metagenomics & Binning (Lecture slides)
- Jakob Nissen
- 14.00-16.00
- Exercise: Metagenomic de novo assembly (Metagenomic assembly exercise) (Metagenomic assembly solution)
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
Thursday, June 13
Quantitative Metagenomics and Test
- 9.00-9.45
- Lecture: Quantitative Metagenomics (Lecture slides)
- Gisle Vestergaard
- 9.45-10.00
- Break
- 10.00-12.00
- Exercise: Quantitative Metagenomics (Exercise) (Solution)
- Gisle Vestergaard, Jakob Nissen
- 12.00-13.00
- Lunch Break
- 13.00-13.45
- Recap Test (Test)
- 13.45-14.00
- Break
- 14.00-16.00
- Time to work on this weeks exercises
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
Friday, June 14
RNA-seq and Cancer-seq
Monday, June 17
Ancient DNA & Tech talks
- 9.00-10.00
- Ancient DNA (Lecture slides)
- Martin Sikora
- 10.00-12.00
- Exercise: Ancient DNA (Exercise)
- Martin Sikora, Gisle Vestergaard
- 12.00-13.00
- Lunch Break
- 13.00-16.00
- Tech talk work & Presentations
- Gisle Vestergaard
Tuesday, June 18
Project work
- 9.00-9.45
- Projects & Group formation (Lecture slides Examples from previous courses)
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
- 9.45-10.45
- Projects & Group formation
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
- 10.45-11.00
- Break
- 11.00-12.00
- Project work
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
- 12.00-13.00
- Lunch Break
- 13.00-16.00
- Project work/Prepare presentations for tomorrow
Wednesday, June 19
Project work & Project Presentations
- 9.00-12.00
- Project work
- Gisle Vestergaard, Katrine Højholt
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Project Presentations
- Gisle Vestergaard
Thursday, June 20
Project work
- 9.00-16.00
- Project work
- 13.00-15.00
- Project work/Office hours
- Gisle Vestergaard, Katrine Højholt
Friday, June 21
Project work
- 9.00-16.00
- Project work
- 13.00-15.00
- Project work/Office hours
- Jose Izarzugaza (Txema), Katrine Højholt
Monday, June 24
Project work
- 9.00-16.00
- Project work
- 13.00-15.00
- Project work/Office hours
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
Tuesday, June 25
Project work
- 9.00-16.00
- Project work
- 13.00-15.00
- Project work/Office hours
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
Wednesday, June 26
Project Work & Poster Printing
- Print your poster, it is possible to print in DTU library for 16-30kr.
- Poster guide & requirements
- 10.00-12.00
- Q&A: Practical information about the Exam
- Project work/Office hours
- Gisle Vestergaard, Jakob Nissen, Katrine Højholt
Thursday, June 27
Poster session - in the hall in front of the Section for Bioinformatics (building 208)
- 10.00-14.00
- Poster session part (exam)