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

Monday 4th
Room: Trippelrummet, E10, ground floor
09.00-09.15 Registration and Welcome, presentation of SciLifeLab (Björn Nystedt)
09.15-10.00 Lecture: Introduction to Linux (Anders Sjölander)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö + Anders Sjölander, Jacques Dainat)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: Introduction to UPPMAX (Anders Sjölander)
14.00-17.00 Exercise: Introduction to UPPMAX (Martin Dahlö + Anders Sjölander, Jacques Dainat)

Tuesday 5th
Room: Trippelrummet, E10, ground floor
09.00-09.30 Lecture: File types in bioinformatics (Martin Dahlö)
09.30-12.00 Exercise: File types in bioinformatics (Martin Dahlö + Anders Sjölander, Jacques Dainat)
12.00-13.00 Lunch at BMC restaurant
13:00-14:00 Lecture: Advanced Linux usage (Martin Dahlö)
14:00-17:00 Exercise: Advanced Linux usage (Martin Dahlö + Anders Sjölander, Jacques Dainat)

Wednesday 6th
Room: Trippelrummet, E10, ground floor
09.00-11.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Petterson)
11.00-12.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: NGS workflow (Anna Johansson)
14.00-17.00 Exercise: NGS workflow part I (Anna Johansson + Payam Emami, Erik Fasterius, Ashfaq Ali)

18:00- Course dinner

Thursday 7th
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: NGS workflow part II (Anna Johansson + Payam Emami, Paulo Czernawski, Ashfaq Ali)
12.00-13.00 Lunch at BMC restaurant
13.00-14:00 Lecture: Data management (Niclas Jareborg)
14.00-14:15 Lecture: RNA sequencing, transcriptome and expression quantification (html, pdf) (Roy Francis)
14.15-17:00 Lecture+Exercise: RNA sequencing, transcriptome and expression quantification (html, pdf) (Roy Francis + Payam Emami, Paulo Czernawski, Ashfaq Ali)

Friday 8th
Room: Trippelrummet, E10, ground floor
09:00-12:00 Lecture+Exercise: RNA sequencing, transcriptome and expression quantification part (html, pdf) (Roy Francis + Payam Emami, Paulo Czernawski, Ashfaq Ali, Erik Fasterius)
12.00-13.00 Lunch at BMC restaurant
13.00-13.20 Lecture: The Bioinformatics Infrastructure in Sweden (Björn Nystedt)
13:20-15.00 Parellel Session 1: Lecture+Exercise: RNA sequencing, transcriptome and expression quantification, continued (Roy Francis + Payam Emami, Paulo Czernawski, Erik Fasterius)
13:20-15.00 Parellel Session 2: Open discussions (Olga Vinnere Pettersson, Sebastian DiLorenzo, Manfred Grabherr, Henrik Lantz, Anna Johansson)