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

Monday 12th
Room: Trippelrummet, E10, ground floor
09.00-09.15 Registration and Welcome, presentation of SciLifeLab (Alice Sollazzo)
09.15-10.00 Lecture: Introduction to Linux (Valentin Georgiev)
10.00-12.00 Exercise: Introduction to Linux (Valentin Georgiev + Jacques Dainat, 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 + Jacques Dainat, Anders Sjölander)

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

Wednesday 14th
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 + Markus Mayrhofer (14-15), Malin Larsson, Diana Ekman )

18:00- Course dinner, Uppsala

Thursday 15th
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: NGS workflow part II (Sebastian DiLorenzo + Markus Mayrhofer, Malin Larsson, Diana Ekman)
12.00-13.00 Lunch at BMC restaurant
13.00-14:00 Lecture: Data management (Niclas Jareborg)
14.00-15:00 Lecture: RNA sequencing, transcriptome and expression quantification (Anna Johansson)
15.00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Anna Johansson + Per Unneberg, Jakub Orzechowski Westholm, Marcel Martin)

Friday 16th
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Anna Johansson + Per Unneberg, Jakub Orzechowski Westholm)
12.00-13.00 Lunch at BMC restaurant
13.00-13.20 Lecture: The Bioinformatics Infrastructure in Sweden (Henrik Lantz)
13:20-15.00 Open discussions (Olga Vinnere Pettersson, Manfred Grabherr, Henrik Lantz, Anna Johansson, Sebastian DiLorenzo)