Health Data Lab

The lab was formerly called the Biological Data Processing Systems (BDPS) Lab.

The big data era in molecular biology has created exiting potential for novel biological discoveries, but also exciting challenges for computer scientists in data management, analysis, and interpretation. Especially exciting are the possibilities in combining omics data with medical images and phenotype variables. Therefore, in the next decades there will be developed sophisticated bioinformatics and machine learning methods and framework to analyze and explore the information in the integrated data. However, the dataset sizes and complexity requires the development of novel infrastructure systems, analysis approaches, and data exploration tools targeted for such complex health datasets.

Our goal is to provide the systems, methods, and tools needed to analyze and interpret complex health datasets. Our research interests are threefold. First, build and experimentally evaluate infrastructure systems for bioinformatics and machine learning analyses. Second, apply bioinformatics, statistics, and machine learning methods for novel health data analyses. Third, build and evaluate data exploration and interpretation tools. All our research is interdisciplinary. We therefore combine experimental computer science with real problems, applications, and data obtained from our biomedical research collaborators.

We also contribute to research infrastructure development and operation, commercialization of our research, and many outreach activities.

Projects

We participate in several large and small projects.

NOWAC

The Norwegian Woman and Cancer (NOWAC) biobank contains time series with questionnaire data from 170 000 women and more than 60 000 blood samples. The biobank is analyzed using several omics technologies including microarrays, RNA-seq, methylation, and mass spectrometry. The data is being analyzed by the Systems Epidemiology group lead by Professor Torkjel Sandanger at the Department of Community Medicine, University of Tromsø. Our responsibility in the project is to build a backend for standardized data analysis pipelines, machine learning based data analysis, and a system for exploration and visualization of the analysis results. We are using these as building blocks to build a platform for swift exploration of the data under different epidemiological designs.

We are also collaborating with Professors Lill-Tove Busund and Tom Dønnem from the Translational Cancer Research Group on multi-level and multi-tissue analysis and clinical use of data from NOWAC.

High North Population Studies

We are members of the strategic initiative High North Population Studies at UiT that combines epidemiological research and computer science to collect, analyze, and utilize the data collected in population studies at UiT. Our contributions are methods to uncover complex cross-level interactions in large heterogeneous population-study datasets, a framework for exploration of metagenomics data integrated with host genomics and phenotype data, and developing and operating infrastructure for bioinformatics analyses on sensitive data.

In the Tromsø Lung Sounds project we are building a database with more than 18.000 lung sound recordings. The recordings are done as part of Tromsøundersøkelsen 7, which is an Epidemiological study that was started in 1974. The database will be used to provide educational and analysis services for lung sounds. Our contributions are methods for automated classification and similarity search for the sounds. This project is done in collaboration with Hasse Melbye at the Department of Community Medicine, University of Tromsø. The results from this project are further developed by our Medsensio AS startup.

In the new Center for New Antibacterial Strategies (CANS) we are responsible for bioinformatics analyses and system biologi.

air:bit

In the air:bit air pollution project we have developed educational projects for use in Norwegian High Schools. This work is done in collaboration with Skolelaboratoriet i realfag og teknologi. We provide build instructions, programming guides, and a portal for data analysis and live visualization. Air:bit has been used by 13 high-school classes in Northern Norway.

Other

Kodeklubben Tromsø is an after-school club for kids and youth who want to learn about computer programming. Together with volunteers from local tech companies and students from our department, members of our lab organize the activities. Each semester we run a 10-week program with two-hour classes each week. In the spring of 2016 we have over 130 kids from ages 7 to 17 attending the club.

We are collaborating with Associate Professor Kristian Svendsen on analysis of adverse drug effect data, and with The Norwegian Historical Data Centre on transcription of Norwegian handwritten census books.

People

The lab currently consist of:

Lars Ailo Bongo Professor Principal investigator Homepage | GitHub | Bitbucket
Edvard Pedersen Associate Professor
Einar Holsbø Postdoc Popultation studies in the north Homepage | GitHub
Morten Grønnesby Ph. D. student NOWAC Homepage | GitHub
Jo Inge Arnes Ph. D. student NOWAC Homepage | --> GitHub
Tengel Skar Master student Adverse drug effect data Homepage | GitHub
Nikita Shvetsov Technical staff Population studies in the north Bitbucket

Former lab members are:

.
Mayeul Marcadella Technical staff ELIXIR.
Aleksandr Agafonov Technical staff ELIXIR.
Dr. Bjørn Fjukstad PhD student, 2018, CS, UiT Thesis: "Toward Reproducible Analysis and Exploration of High-Throughput Biological Datasets." and source code for Kvik and walrus.
Tim Alexander Teige Master student, 2018, CS, UiT Thesis: Auto scaling framework, simulator, and algorithms for the META-pipe backend and Source code.
Nina Angelvik Master student, 2018, CS, UiT Thesis: Data management platform for citizen science education projects. Source code: Backend and Frontend
Mike Voets Master student, 2018, CS, UiT Thesis: Deep Learning: From Data Extraction to Large-Scale Analysis. Source code: replication study and DICOM anonymizer.
Inge Alexander Raknes Technical staff ELIXIR.
Rigmor Katrine Johansen Intern, 2017 Bioethics, NOWAC
Johan Ravn Master student, 2017, CS, UiT Thesis: Detection of Wheezes and Breathing Phases using Deep Convolutional Neural Networks.
Dr. Giacomo Tartari Technical staff ELIXIR
Frode Opdahl Master student, 2016, CS, UiT Project: Virtual reality.
Jarl Fagerli Master student, 2015, CS, UiT Thesis: COMBUST I/O. Abstractions facilitating parallel execution of programs implementing common I/O patterns in a pipelined fashion as workflows in Spark. Thesis. Source code.
Kenneth Knudsen Master student, 2015, CS, UIT Thesis: Freia: Exploring Biological Pathways Using Unity3D. (Thesis, Source Code, Demo)
Ove Kåven Master student, 2015, CS, UiT Thesis: Multiparadigm Optimizing Retargetable Transdisciplinary Abstraction Language (Thesis, Source code)
Ida Jaklin Johansen Technical staff Elixir.no
Martin Ernstsen Master student, 2013, CS, UiT Thesis: Mario - A system for iterative and interactive processing of biological data (Thesis, Source code)
Terje André Johansen Master student, 2011, CS, UiT Thesis: A scalable, interactive widget library for visualizing biological data (Thesis, Paper)
Torje Henriksen Master student (main-advisor Otto J. Anshus, co-advisor Phuong Hoai Ha), 2008, CS, UiT Thesis: Efficient intra-node Communication for Chip Multiprocessors

Collaborators

We are a lab in the High Performance Distributed Systems research group at the Department of Computer Science, University of Tromsø.

We are also part of the Center for Bioinformatics which is co-located with the Norwegian Structural Biology Centre (NORSTRUCT).

We collaborate with Professor Eiliv Lund, Torkjel Sandanger, Lill-Tove Busund, and Tom Dønnem in the NOWAC project.

We collaborate with Professor Hasse Melbye in the Lung Sounds project.

EPINOR is a national research school in population based epidemiology. We are one of associated research groups, and our PhD students can apply for admission to the school.

NORBIS is the national research school for bioinformatics, biostatistics, and systems biology.

We have long term collaboration with Professors Kai Li and Olga Troyanskaya at Princeton University. We are also collaborating with Etienne Birmelé at Université Paris Descartes.