Click the heading of a topic to see the lecture slides or lab instructions. Slides are added as the course progresses.

Monday 27th
Room: Trippelrummet, E10, ground floor
09.00-09.15 Registration and Welcome, presentation of SciLifeLab (Elina Staaf)
09.15-10.00 Lecture: Introduction to Linux (Valentin Georgiev)
10.00-12.00 Exercise: Introduction to Linux (Valentin Georgiev + Nina Norgren, Markus Mayrhofer, Anders Sjölander)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: Introduction to UPPMAX (Valentin Georgiev)
14.00-17.00 Exercise: Introduction to UPPMAX (Valentin Georgiev + Nina Norgren, Per Unneberg, Anders Sjölander)

Tuesday 28th
Room: Trippelrummet, E10, ground floor
09.00-09.30 Lecture: File types in bioinformatics (Jacques Dainat)
09.30-12.00 Exercise: File types in bioinformatics (Jacques Dainat + Nina Norgren, Markus Mayhofer, Anders Sjölander)
12.00-13.00 Lunch at BMC restaurant
13:00-14:00 Lecture: Advanced Linux usage (Jacques Dainat)
14:00-17:00 Exercise: Advanced Linux usage (Jacques Dainat + Nina Norgren, Bengt Sennblad, Anders Sjölander)

Wednesday 29th
Room: Trippelrummet, E10, ground floor
09.00-11.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
11:00-12.00 Lecture: NGS and bioinformatics analysis pipelines (Olga Vinnere Pettersson)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: NGS workflow (Sebastian DiLorenzo)
14.00-17.00 Exercise: NGS workflow part I (Sebastian DiLorenzo + Nina Norgren, Verena Kutschera, John Sundh)

18:00- Course dinner at Koh Phangan, Övre Slottsgatan 12, Uppsala

Thursday 30th
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: NGS workflow part II (Sebastian DiLorenzo + Jacques Dainat, Mahesh Binzer- Panchal, Lucile Soler)
12.00-13.00 Lunch at BMC restaurant
13.00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Olga Dethlefsen)
14.00-15:00 Lecture: Data management (Niclas Jareborg)
15.00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Olga Dethlefsen + Sebastian DiLorenzo, Jacques Dainat)

Friday 1st
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Diana Ekman, John Sundh, Lucile Soler)
12.00-13.00 Lunch at BMC restaurant
13.00-13.20 Lecture: The Bioinformatics Infrastructure in Sweden (Björn Nystedt)
13:20-15.00 Open discussions (Manfred Grabherr, Diana Ekman, John Sundh)