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

Monday 9th
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 (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö + Anders Sjölander, Jacques Dainat, Payam Emami)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: Introduction to UPPMAX (Martin Dahlö)
14.00-17.00 Exercise: Introduction to UPPMAX (Martin Dahlö + Anders Sjölander, Jacques Dainat, Payam Emami)

Tuesday 10th
Room: Trippelrummet, E10, ground floor
09.00-09.30 Lecture: File types in bioinformatics (Anders Sjölander)
09.30-11.00 Exercise: File types in bioinformatics (Anders Sjölander + Martin Dahlö, Jacques Dainat, Payam Emami)
11.00-12.00 Lecture: Improving your terminal experience (Anders Sjölander)
12.00-13.00 Lunch at BMC restaurant
13:00-14:00 Lecture: Advanced Linux usage (Anders Sjölander)
14:00-17:00 Exercise: Advanced Linux usage (Anders Sjölander + Martin Dahlö, Jacques Dainat, Payam Emami)

Wednesday 11th
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 (Anna Johansson)
14.00-17.00 Exercise: NGS workflow (Anna Johansson + Payam Emami, Lucile Soler, Markus Mayrhofer, Per Unneberg)

18:00- Course dinner at Koh Phangan (Fyristorg 2, next to the river)

Thursday 12th
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: NGS workflow (Anna Johansson + Payam Emami, Nima Rafati, Markus Mayrhofer, Lucile Soler)
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 (html, pdf) (Johan Reimegård)
15.00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification (html, pdf) (Johan Reimegård + Mahesh Panchal, Payam Emami, Bengt Sennblad, Per Unneberg)

Friday 13th
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification (html, pdf) (Johan Reimegård + Mahesh Panchal, Nima Rafati, Payam Emami, Per Unneberg)
12.00-13.00 Lunch at BMC restaurant
13.00-13.20 Lecture: The Bioinformatics Infrastructure in Sweden (Björn Nystedt)
13:20-15.00 Parallel session 1: Exercise: RNA sequencing, transcriptome and expression quantification, continued (Mahesh Panchal, Nima Rafati, Payam Emami, Per Unneberg)
13:20-15.00 Parallel session 2: Open discussions (Olga Vinnere Pettersson, Anna Johansson, Jacques Dainat)