Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics fall 2018¶
Note: for previous course editions (INF-BIO9121 and INF-BIO5121), check out this website.
This is the webpage for the fall 2018 edition of the credited courses IN-BIOS5000 (master level) and IN-BIOS9000 (Ph.D. level) offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO) and funded by NORBIS.
This course consists of two weeks, of lectures and practicals, and a final take-home exam, plus a written exam on the course material and the reading material.
Course days are usually from 9:15 to 17:00 (teachers may stay longer if requested), some lectures, mostly hands-on exercises. All materials for lectures and practicals will be linked from the schedule below.
The schedule will appear here early in August and will link to the webpages with the material taught (these links are added as the course progresses).
|Day||Room||Morning (09:15-12:00)||Afternoon (13:00-17:00)|
|Mon. Oct. 22||Shell||Update on NORBIS
Fundamentals of Molecular Biology
|HTS & applications
|Tue. Oct. 23||Postscript||Oxford Nanopore technology
|Basic file formats|
|Wed. Oct. 24||Shell||Pre-processing of HTS data||Algorithms|
|Thu. Oct. 25||Java||Algorithms||De novo assembly
Dinner @1800 hrs in Olivia, Aker brygge
|Fri. Oct. 26||Java||De novo assembly||De novo assembly|
|Mon. Oct. 29||Shell||De novo assembly||De novo assembly|
|Tue. Oct. 30||Postscript||Variant calling||Variant calling|
|Wed. Oct. 31||Python||Variant calling||Variant calling|
|Thu. Nov. 01||Python||Statistical genomics||Statistical genomics|
|Fri. Nov. 02||Python||Statistical genomics||Statistical genomics|
|Thu. Nov. 29||TBA||Oral exam||Oral exam|
|Fri. Nov. 30
Ole-Johan Dahls hus location: Google maps
- Shell: room 1456 Informatics building (Ole-Johan Dahls hus)
- Postscript: room 2458 Informatics building (Ole-Johan Dahls hus)
- Java: room 2423 Informatics building (Ole-Johan Dahls hus)
- Python: room 2269 Informatics building (Ole-Johan Dahls hus)
Dinner on Oct 25
Written exam will take place on Nov 30 at 1430 hrs (2 hour exam) in Store fysiske lesesal Fysikkbygningen
- We recommend that participants should have a basic understanding of molecular biology as provided by an introductory course in bioinformatics, molecular biology, or genetics.
- No formal background in computer science is required, however, students must have a basic understanding of the unix shell. Students should take an introductory unix course beforehand if they do not have these skills.
Computers/laptops, internet access, and UiO user account¶
All students must bring a laptop with either a Windows (Windows 7 or more recent), Unix/Linux, or OS X (i.e. an Apple computer) operating system.
- The computer should not be more than 2-3 years old
- It should be possible to connect the computer to the UiO wireless network
- You must have modern internet browser installed (Chrome, Firefox, Safari, …)
- You must have a valid UiO user account and must be able to log onto a computer on the UiO network
- We advise to bring an external mouse, and do not rely on touchpad/trackpad only
If you are struggling with anything of the above, in particular if you have forgotten your UiO user name/password or you do not have one, you must contact the course coordinator (see contact details on this page) as soon as possible, and at least one week before the start of the course.
Curriculum and suggested reading¶
The curriculum consists of a set of scientific articles. The exam will contain questions on the material presented in these papers on the material covered during the course. Specific details of the curriculum, and a list of further suggested papers, can be found here.
The exam for this course will be:
- a written exam on the course and curriculum, time and place to be announced
- an individual, home exam combined with an oral examination of the home exam time, and place to be announced. Students will present their work to two-three teachers, followed by some questioning (20-30 minutes in total). This home exam will be handed out to all participants during the last course day.
NOTE Both exams have to be passed to earn study credits.
NOTE 80% attendance is required to take the final exam.
- Arvind Sundaram (Course coordinator) - e-mail: arvind.sundaram - at -medisin.uio.no
- Course administration/registration - e-mail: email@example.com
- Arvind Sundaram (AS, Bioinformatician, Norwegian Sequencing Centre, Oslo University Hospital)
- Ave Tooming-Klunderud (AT, CEES, Faculty of Mathematics and Natural Sciences, University of Oslo)
- Gregor Gilfillan (GG, Researcher, Norwegian Sequencing Centre, Oslo University Hospital)
- Ivar Grytten (IG, Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)
- Karin Lagesen (KL, Section for Epidemiology, Norwegian Veterinary Institute)
- Ragna Breines (Coordinator, NORBIS)
- Thomas Haverkamp (KL, Section for Epidemiology, Norwegian Veterinary Institute)
- Timothy Hughes (TH, Researcher, NORMENT , Oslo University Hospital)
- Torbjørn Rognes (TR, Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)