IN-BIOS5000 / IN-BIOS9000 Autumn 2024¶
Sequencing technologies, data analysis and applications¶
The information below is preliminary and will be updated. In particular, the exact dates are uncertain.
Introduction¶
Here you will find information about the autumn 2024 edition of the credited courses IN-BIOS5000 (MSc level) and IN-BIOS9000 (PhD level), on Sequencing technologies, data analysis and applications. The course is offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO) in collaboration with contributors from Oslo University Hospital and the Norwegian Veterinary Institute. It is partially funded by the NORBIS, the national research school in bioinformatics, biostatistics and systems biology. This course consists of two weeks of lectures and practicals, a home project with an oral exam presentation, and a digital written exam.
Audience¶
The course is open for master and PhD students at UiO, as well as to PhD students registered through the NORBIS national research school. To earn credits for the course, PhD students from other institutions than UiO must obtain the status as a visiting PhD candidate at the UiO Faculty of Mathematics and Natural Sciences. Applications may be submitted starting 14 June 2024 and must be submitted by 1 August 2024. A maximum of 30 students in total will be admitted to the course.
Course content¶
The course provides knowledge of sequencing technologies and hands-on experience with the analysis of data from several current sequencing platforms and for various biological and medical applications. Tools, algorithms, and statistical methods for data analysis will be included, as well as data quality assessment and analysis reproducibility. The applications that will be covered may vary from year to year but will typically include de novo whole-genome assembly and variant calling. Other applications like RNA-Seq, ChIP-Seq, or metagenomics could also be covered.
Learning outcome¶
After completing this course, you will:
understand the differences, benefits, and drawbacks of the current sequencing technologies, and be able to decide which platform to use in what way for the different applications
be able to evaluate sequencing data quality and quantity
know the tools, algorithms, and statistical methods involved in the data analysis
be able to perform bioinformatics analysis with data tailored towards selected applications
be able to report on the data analysis in such a way that the methods used and the steps taken are transparent, thus enhancing reproducibility
be aware of, and know to deal with, the ethical and data-sensitivity issues surrounding sequencing data derived from human subjects
be able to critically evaluate, validate and judge the results of bioinformatics analysis of sequencing experiments in terms of underlying assumptions, reliability, sensitivity and specificity, and evaluate their value for answering biological questions
Location¶
The course will be held at the UiO campus, in seminar room 2269 Python (not confirmed), on floor 2 in the northern end of Ole-Johan Dahl’s building, Gaustadalléen 23B, Oslo.
Schedule (preliminary)¶
Lectures and practical sessions will be held Monday to Friday, October 28th to November 8th, 2024 (weeks 44 and 45) (not confirmed). Course days are usually from 09.15 to 17.00. There will be a lunch break each day from 12.00 to 13.15.
In the table below, teachers are indicated with their initials and listed in the following section. A teaching assistant will help during the exercises.
Time |
Session (Teacher) |
|---|---|
Week 44 |
|
Mon 28 Oct |
|
09.15 - 09.30 |
Welcome and practical information (TR) |
09.30 - 12.00 |
Fundamentals of Molecular Biology (RS) |
12.00 - 13.15 |
Lunch break |
13.15 - 14.00 |
Sequencing and applications (TR) |
14.15 - 15.00 |
Illumina sequencing technology (AS) |
15.15 - 16.00 |
PacBio sequencing technology (ATK) |
Tue 29 Oct |
|
09.15 - 10.00 |
Oxford Nanopore sequencing technology (TH) |
10.15 - 12.00 |
Library preparation (AS) |
12.00 - 13.15 |
Lunch break |
13.15 - 15.00 |
Basic file formats (AS) |
15.15 - 17.00 |
Access to computational resources (TR) |
Wed 30 Oct |
|
09.15 - 12.00 |
Data preprocessing (AS) |
12.00 - 13.15 |
Lunch break |
13.15 - 17.00 |
TBA |
Thu 31 Oct |
|
09.15 - 12.00 |
De novo genome assembly (KL) |
12.00 - 13.15 |
Lunch break |
13.15 - 17.00 |
De novo genome assembly, continued |
19.00 - 22.00 |
Dinner at restaurant |
Fri 1 Nov |
|
09.15 - 12.00 |
De novo genome assembly, continued |
12.00 - 13.15 |
Lunch break |
13.15 - 17.00 |
De novo genome assembly, continued |
|
|
Week 45 |
|
Mon 4 Nov |
|
09.15 - 12.00 |
Introduction to variant calling (BS) |
12.00 - 13.15 |
Lunch break |
13.15 - 15.00 |
Variant calling in general, continued (BS) |
15.15 - 17.00 |
Human germline variant calling (YS) |
Tue 5 Nov |
|
09.15 - 12.00 |
Human germline variant calling, continued (YS) |
12.00 - 13.15 |
Lunch break |
13.15 - 16.00 |
Somatic variant calling and interpretation in the context of cancer (SN) |
Wed 6 Nov |
|
09.15 - 12.00 |
Microbiome analysis (NKN) |
12.00 - 13.15 |
Lunch break |
13.15 - 17.00 |
Multi-omic network analysis (NKN) |
Thu 7 Nov |
|
09.15 - 12.00 |
Transcriptomics (RS) |
12.00 - 13.15 |
Lunch break |
13.15 - 17.00 |
Small RNA transcriptomics (TBR) |
Fri 8 Nov |
|
09.15 - 12.00 |
Machine learning in computational biology (MP) |
12.00 - 13.15 |
Lunch break |
13.15 - 16.00 |
Machine learning in computational biology, continued (MP) |
16.00 - 16.15 |
Exam info and course evaluation (TR) |
16.15 - 17.00 |
Pizza on campus |
|
|
Week 50 |
|
Thu 12 Dec |
|
09.15 - 15.00 |
Oral presentation and exam |
17.00 - 19.00 |
Written exam |
Fri 13 Dec |
|
09.15 - 15.00 |
Oral presentation and exam |
Teachers¶
Initials |
Name |
Affiliation |
|---|---|---|
AS |
Arvind Sundaram |
Norwegian Sequencing Centre, Oslo University Hospital |
ATK |
Ave Tooming-Klunderud |
CEES, Dept. of Biosciences, University of Oslo |
BS |
Bastiaan Star |
CEES, Dept. of Biosciences, University of Oslo |
KL |
Karin Lagesen |
Section for Epidemiology, Norwegian Veterinary Institute |
MP |
Milena Pavlovic |
Centre for Bioinformatics, Dept. of Informatics, University of Oslo |
NKN |
Nolan Keith Newman |
Centre for Molecular Medicine Norway (NCMM), University of Oslo |
RS |
Rolf Skotheim |
Centre for Bioinformatics, Dept. of Informatics, University of Oslo |
SN |
Sigve Nakken |
Oslo University Hospital |
TH |
Thomas Haverkamp |
Section for Epidemiology, Norwegian Veterinary Institute |
TR |
Torbjørn Rognes |
Centre for Bioinformatics, Dept. of Informatics, University of Oslo |
TBR |
Trine B. Rounge |
Centre for Bioinformatics, Dept. of Pharmacy, University of Oslo |
YS |
Ying Sheng |
Dept. of Medical Genetics, Oslo University Hospital |
Contact information¶
Torbjørn Rognes (Course coordinator), email torognes@ifi.uio.no
Meals¶
Coffee and tea will be freely available each morning in the seminar room.
For lunch, we recommend the canteen in the other end of the building, Ole-Johan eatery, which serves a nice selection of warm and cold dishes.
We are organizing a free dinner for all course participants at a restaurant some day during the course.
We will also order pizza one afternoon.
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.
Computing facilities¶
All students must have a laptop with either Windows (version 10 or more recent), macOS, Linux or other Unix operating system. You need to be able to access the Eduroam wifi network. If you do not have a UiO or Eduroam account, a temporary Wifi account may be created for you. We advise you to bring an external mouse, and do not rely on touchpad/trackpad only.
The course will use computational resources on the Educloud Fox system at UiO. Access to Educloud will be provided for all course participants. A list of the software packages that will be used is available.
If you are struggling with anything of the above, 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 will be a combination of the following two parts:
an individual home project combined with an oral exam presentation of the home project followed by questioning / discussion on December 12th and 13th (not confirmed). Students will present their work to 2-3 teachers, followed by some questioning (approx 20 minutes in total for each student). This home exam will be handed out to all participants after the lectures.
a 2 hour written digital exam at Silurveien 2 on December 12th or 13th (date not confirmed)
The exams are graded on a pass/fail scale.
Written exams from previous years:
There was no written exam in 2020 due to the pandemic.
Lecture slides¶
Teaching materials¶
List of further suggested papers, can be found here.
Previous editions of the course¶
Note: For previous editions of the IN-BIOS5000 / IN-BIOS9000 course please see the 2018, 2020, or 2022 websites. The course was not held in 2019 and 2021. For previous editions of the INF-BIO9121 and INF-BIO5121 course, please see the 2013, 2014, 2015, 2016 or 2017 website. The 2012 version did not have a dedicated available website.