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

Monday 15th
Room: Ingegerd Eriksson
10.00-10.15 Registration and Welcome, presentation of SciLifeLab (Elina Staaf, Magnus Alm Rosenblad)
10.15-11.00 Lecture: Introduction to Linux (Valentin Georgiev)
11.00-12.00 Exercise: Introduction to Linux (Valentin Georgiev, Martin Dahlö, Marcela Davila Lopez, Magnus Alm Rosenblad)
12.00-13.00 Lunch
13.00-14.00 Lecture: Introduction to UPPMAX/UPPNEX ( Valentin Georgiev)
14.00-17.00 Exercise: Introduction to UPPMAX/UPPNEX (Valentin Georgiev, Martin Dahlö, Marcela Davila Lopez, Magnus Alm Rosenblad)

Tuesday 16th
Room: Ingegerd Eriksson
09.00-09.30 Lecture: File types in bioinformatics (Martin Dahlö)
09.30-12.00 Exercise: File types in bioinformatics (Valentin Georgiev, Marcela Davila Lopez, Martin Dahlö, Magnus Alm Rosenblad)
12.00-13.00 Lunch
13:00-14:00 Lecture: Advanced Linux usage (Martin Dahlö)
14:00-17:00 Exercise: Advanced Linux usage (Valentin Georgiev, Marcela Davila Lopez, Martin Dahlö, Magnus Alm Rosenblad)

Wednesday 17th
Room: Ingegerd Eriksson
09:00-10.00 Lecture: NGS workflow (Sebastian DiLorenzo)
10:00-12.00 Exercise: NGS workflow part I (Sebastian DiLorenzo, Katarina Truvé, Magnus Alm Rosenblad)
12.00-13.00 Lunch
13.00-17:00 Exercise: NGS workflow part II (Sebastian DiLorenzo, Lena Hansson, Magnus Alm Rosenblad)

18:00- Course dinner at Taverna Averna

Thursday 18th
Room: Birgit Thilander 9-12, thereafter Ingegerd Eriksson
09.00-11.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
11:00-12.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
12.00-13.00 Lunch
13.00-14.00 Lecture: RNA sequencing, transcriptome and expression quantification (Lena Hansson)
14.00-17.00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Leif Väremo, Lena Hansson, Sebastian DiLorenzo)

Friday 19th
Room: Ingegerd Eriksson
09:00-10:00 Lecture: Data management (Niclas Jareborg)
10:30-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Leif Väremo, Lena Hansson, Sebastian DiLorenzo, Niclas Jareborg)
12.00-13.00 Lunch
13.00-13.20 Lecture: The Bioinformatics Infrastructure in Sweden (Niclas Jareborg)
13:20-15.00 Open discussions (Leif Väremo, Sebastian DiLorenzo, Katarina Truvè)