Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics fall 2020¶
IN-BIOS5000 and IN-BIOS9000¶
Note: for previous course editions (INF-BIO9121 and INF-BIO5121), check out this website.
Lecture slides¶
Lecture slides
This page is updated after each lecture/Module.
Introduction¶
This is the webpage for the fall 2020 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 with oral presentation and questioning.
Schedule¶
Course days are usually from 9:15 to 17:00, with lectures and hands-on exercises.
Room location:
| Day | Time | Session |
|---|---|---|
| Week 43 | ||
| Mon. Oct. 19 | 09:15-09:30 09:30-12:00 13:00-14:30 14:45-15:30 15:45-16:30 |
Update on NORBIS (RB) Fundamentals of Molecular Biology (GG) HTS & applications (TR) (pre-recorded) Illumina sequencing (AS) PacBio technology (AT) |
| Tue. Oct. 20 | 09:15-10:00 10:15-10:45 11:00-12:00 13:00-13:45 14:00-16:00 |
Oxford Nanopore technology (THa) (pre-recorded) Library preparation (AS) Experimental design (AS) Access to UiO and compute Basic file formats (AS) |
| Wed. Oct. 21 | 09:15-12:00 13:00-17:00 |
Pre-processing of HTS data (AS) Algorithms (THu) |
| Thu. Oct. 22 | 09:15-12:00 13:00-16:00 |
Algorithms (THu) De novo assembly (KL) |
| Fri. Oct. 23 | 09:15-16:00 | De novo assembly (KL) |
| Week 44 | ||
| Mon. Oct. 26 | 09:15-16:00 | De novo assembly (KL) |
| Tue. Oct. 27 | 09:15-16:00 | Statistical genomics (IG) |
| Wed. Oct. 28 | 09:15-16:00 | Statistical genomics (IG) |
| Thu. Oct. 29 | 09:15-16:00 | Introduction to machine learning in computational biology (MP) |
| Fri. Oct. 30 | 09:15-12:00 13:00-14:00 14:15-15:15 15:30-16:00 |
Small RNA transcriptomics (TBR) Introduction to somatic variant calling (DV) Interpretation of DNA variation in the context of cancer (SN) Exam info and course evaluation |
| Week 48 | ||
| Thu. Nov. 26 | TBA | Oral exam |
| Fri. Nov. 27 | TBA | Oral exam |
Room location:
All activities will be carried out on Zoom. Zoom info will be distributed by email.
Exam location:
Exam: Oral presentation of home exam and questioning on Nov 26 and 27 by Zoom. Zoom info will be distributed by email.
Requirements¶
- 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 have 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
- 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.
Exam¶
The exam for this course will be an individual home exam combined with an oral presentation of the home exam and questioning on Zoom on 26/27 November. Exact time 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 in the week after the lectures.
Contact information¶
- Arvind Sundaram (Course coordinator) - e-mail: arvind.sundaram - at -medisin.uio.no
- Course administration/registration - e-mail: studieinfo@ifi.uio.no
Teachers¶
- Arvind Sundaram (AS, Bioinformatician, Norwegian Sequencing Centre, Oslo University Hospital)
- Ave Tooming-Klunderud (AT, CEES, Faculty of Mathematics and Natural Sciences, University of Oslo)
- Daniel Vodak (DV, Oslo University Hospital)
- 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)
- Milena Pavlovic (MP, Dept. of Informatics, University of Oslo)
- Ragna Breines (RB, Coordinator, NORBIS)
- Sigve Nakken (SN, Post.Doc., Oslo University Hospital)
- Thomas Haverkamp (THa, Section for Epidemiology, Norwegian Veterinary Institute)
- Timothy Hughes (THu, Researcher, NORMENT , Oslo University Hospital)
- Torbjørn Rognes (TR, Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)
- Trine B. Rounge (TBR, Researcher, Kreftregisteret)