Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics fall 2022

IN-BIOS5000 and IN-BIOS9000

The information below is preliminary, and some of it has not been updated since 2020.

Note: For previous editions of the INF-BIO9121 and INF-BIO5121 course in 2013-2017, check out [this website](http://inf-biox121.readthedocs.io). For previous editions of the IN-BIOS5000 / IN-BIOS9000 course please see the [2018](https://in-biosx000.readthedocs.io/en/2018/) and [2020](https://in-biosx000.readthedocs.io/en/2020/) versions.

## Introduction

This is the webpage for the fall 2022 edition of the credited courses [IN-BIOS5000](http://www.uio.no/studier/emner/matnat/ifi/IN-BIOS5000) (master level) and [IN-BIOS9000](http://www.uio.no/studier/emner/matnat/ifi/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](https://norbis.w.uib.no/activities/courses/).

This course consists of two weeks, of lectures and practicals, and a final take-home exam with oral presentation and questioning.

## 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](https://www.mn.uio.no/english/research/phd/educational-component/visiting-phd.html) at the UiO Faculty of Mathematics and Natural Sciences. Applications may be submitted starting 15 June 2022 and must be submitted within 1 August 2022.

## Location

The course will be held at the UiO campus, in seminar room 2269 “Python”, on floor 2 in the north end of <a href=”https://www.uio.no/english/about/getting-around/areas/gaustad/ga06/”>Ole-Johan Dahl’s building</a>, Gaustadalléen 23B, Oslo.

## Schedule Course days are usually from 9:15 to 17:00, with lectures and hands-on exercises. There will be a lunch break from 12:00 to 13:15. Coffee and tea will be available each morning in the seminar room.

In the table below, teachers are indicated with their initials and listed in the following section.

Date | Time | Session | Teacher |
—————- | :———–: | ————— | ——- |
Week 42
Monday 17 Oct | 09.15 - 09.30 | Intro to NORBIS | TBA
| 09.30 - 12.00 | Fundamentals of Molecular Biology | GG
| 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
Tuesday 18 Oct | 09.15 - 10.00 | Oxford Nanopore sequencing technology | TH
| 10.15 - 11.00 | Library preparation | AS
| 11.15 - 12.00 | Experimental design | AS
| 12.00 - 13.15 | Lunch break
| 13.15 - 15.00 | Basic file formats | AS
| 15.15 - 17.00 | Access to computational resources | TR
Wednesday 19 Oct | 09.15 - 12.00 | Pre-processing of HTS data | AS
| 12.00 - 13.15 | Lunch break
| 13.15 - 17.00 | De novo genome assembly | KL
Thursday 20 Oct | 09.15 - 12.00 | De novo genome assembly, continued | KL
| 12.00 - 13.15 | Lunch break
| 13.15 - 17.00 | De novo genome assembly, continued | KL
| 20.00 - 22.00 | Dinner at restaurant in Oslo
Friday 21 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 | KL
Week 43
Monday 24 Oct | 09.15 - 12.00 | Variant calling in general | 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
Tuesday 25 Oct | 09.15 - 12.00 | Somatic variant calling and interpretation in the context of cancer | SN
| 12.00 - 13.15 | Lunch break
| 13.15 - 17.00 | Small RNA transcriptomics | TBR
Wednesday 26 Oct | 09.15 - 12.00 | Statistical genomics | IG
| 12.00 - 13.15 | Lunch break
| 13.15 - 17.00 | Statistical genomics, continued | IG
Thursday 27 Oct | 09.15 - 12.00 | Statistical genomics, continued | IG
| 12.00 - 13.15 | Lunch break
| 13.15 - 16.00 | Statistical genomics, continued | IG
| 16.15 - 17.00 | Pizza on campus
Friday 28 Oct | 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
| 16.15 - 16.30 | Exam info and course evaluation | TR

## Teachers

  • 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)

  • GG: Gregor Gilfillan (Norwegian Sequencing Centre, Oslo University Hospital)

  • IG: Ivar Grytten (Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)

  • KL: Karin Lagesen (Section for Epidemiology, Norwegian Veterinary Institute)

  • MP: Milena Pavlovic (Dept. of Informatics, University of Oslo)

  • SN: Sigve Nakken (Oslo University Hospital)

  • TH: Thomas Haverkamp (Section for Epidemiology, Norwegian Veterinary Institute)

  • TR: Torbjørn Rognes (Research Group for Biomedical Informatics / 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)

  • TBA: Others to be announced

## Contact information

## Restaurant dinner & Pizza

We plan to organize a dinner for the course participants in a restaurant in Oslo on October 20th. We also plan to order pizza on October 27th. Details will follow.

## 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, Wifi, internet access, and Educloud accounts

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](Educloud) will be provided for all course participants.

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](Curriculum).

## 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 1st and 2nd. Students will present their work to 2 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. Time slots will be assigned randomly.

  • a 2 hour written digital exam at Silurveien 2 on December 1st 2022 from 17.00 to 19.00.

### Written exams from previous years

## Lecture slides

[Lecture slides](Lectures)<br/>

This page is updated after each lecture/Module.

## Teaching materials

List of further suggested papers, can be found [here](Curriculum).