Click the heading of a topic to see the lecture slides or lab instructions. Slides are added as the course progresses.
Monday 10th
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 (Anders Sjölander, Martin Dahlö, Jacques Dainat)
12.00-13.00 Lunch
13.00-14.00 Lecture: Introduction to UPPMAX (Anders Sjölander)
14.00-17.00 Exercise: Introduction to UPPMAX (Anders Sjölander, Martin Dahlö, Jacques Dainat)
Tuesday 11th
Room: Datorsal A6:003, BMC
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
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 12th
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 (Olga Vinnere Petterson)
12.00-13.00 Lunch
13.00-14.00 Lecture: NGS workflow (Anna Johansson)
14.00-17.00 Exercise: NGS workflow part I (Anna Johansson + Markus Mayrhofer, Diana Ekman, Mahesh Panchal)
18:00- Course dinner
Thursday 13th
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: NGS workflow part II (Anna Johansson + Markus Mayrhofer, Diana Ekman, Mahesh Panchal)
12.00-13.00 Lunch
13.00-14:00 Lecture: Data management (Niclas Jareborg)
14.00-15:00 Lecture: RNA sequencing, transcriptome and expression quantification (html,pdf) (Roy Francis)
15.00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Roy Francis + Per Unneberg, Bengt Sennblad, Adnan Niazi)
Friday 14th
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Roy Francis + Per Unneberg, Bengt Sennblad, Adnan Niazi)
12.00-13.00 Lunch
13.00-13.20 Lecture: The Bioinformatics Infrastructure in Sweden (Björn Nystedt)
13:20-15.00 Open discussions (Olga Vinnere Pettersson, Manfred Grabherr, Björn Nystedt, Anna Johansson, Roy Francis)