Resumé
Education
2017 Msc.Eng. from Technical University of Denmark in “Mathematical Modelling and Computation””
2015 Bsc.Eng. from Technical University of Denmark in “Mathematics and Technology”
Experience
January 2022 - December 2023
Kongsberg Discovery, Uncrewed Platforms
Senior Software Engineer
Formerly known as Marine Robotics, the Uncrewed Platforms division develops an Autonomous Underwater Vehicle affectionately known as Hugin. As part of the Navigation team in the Software Group, my job was to develop the Inertial Navigation System (INS) that enables Hugin to navigate autonomously underwater. Furthermore, we developed post processing and visualization tools to analyze and improve navigation performance post mission.
February 2017 - December 2021
FarGen, The Faroe Genome Project
Bioinformatician / Senior Engineer
My main responsibility at FarGen (https://www.fargen.fo/) was to pre-process and analyze the large amounts of DNA sequencing data coming out of the laboratory.
I have had the privilege and great challenge to design the FarGen Cluster. From the start I tailored the cluster specifically for bioinformatics, from bare metal to user interface. The cluster is based on a powerful compute component managed by Kubernetes, and a efficient and reliable storage component based on Ceph.
In 2018, I applied for research funding from the Research Council Faroe Islands, and was awarded a PhD scholarship. In October of 2021 I decided to discontinue my PhD studies. During this time I took 26 ECTS worth of PhD courses. I also taught a PhD course in statistics in R, where I created the whole course from scratch (olavurmortensen.github.io/r-for-statistics). I practiced my duty to communicate science to both laymen and professionals, both abroad and at home.
In September 2021, I received the new title of Senior Engineer, which was deemed more fitting to my role at FarGen.
2015-2017
RaRe Technologies
Intern
At RaRe Technologies, I was an open source developer for the Gensim project. In one of my projects, I developed a machine learning algorithm from scratch, wrote an efficient implementation, wrote tests through continuous integration, and wrote documentation for it. The tutorial I wrote (link below) was well received by the community. My master’s thesis on the subject (link below) received the highest grade attainable.
Master’s thesis: www2.imm.dtu.dk/pubdb/edoc/imm6971.pdf
2015
FractureCode Corporation
Student assistant
Together with another student, I worked on a project exploring the possibilities in using big data technologies (specifically, Apache Spark) to analyze the huge amounts of data that FractureCode’s customers generate.
2012
Technical University of Denmark
Teaching assistant
I assisted in the group work sessions in two terms of a course, teaching first year engineering students introductory programming in MatLab. I also graded reports in this course, which served as the students’ exams.
Publications
I’m the main author of two peer-reviewed scientific articles.
- Mortensen, Ó., Thomsen, E., Lydersen, L., Apol, K., Weihe, P., Steig, B., Andorsdóttir, G., Als, T. & Gregersen, N. (2022). FarGen: Elucidating the distribution of coding variants in the isolated population of the Faroe Islands. DOI
- Mortensen, Ó., Lydersen, L. N., Apol, K. D., Andorsdóttir, G., Steig, B. á, & Gregersen, N. O. (2019). Using dried blood spot samples from a trio for linked-read whole-exome sequencing. European Journal of Human Genetics. DOI
GitHub portfolio
The Author-Topic Model module in Gensim
I developed the atmodel module for the Gensim Python library.
https://radimrehurek.com/gensim/models/atmodel.html
Tutorial for the atmodel module:
PedGraph
A Python library for multi-layer network representation of pedigrees.
github.com/olavurmortensen/pedgraph
LinkSeq
A pipeline written in Nextflow to process Next-Generation Sequencing linked-read data and perform germline variant discovery.
github.com/olavurmortensen/linkseq
HMS Beagle
A Docker image containing basically everything you need to do bioinformatics. This image is the user environment on the FarGen Cluster.