The increasing use of omics data in epidemiology enables many novel study designs, but also introduces challenges for data analysis. We describe the possibilities for systems epidemiological designs in the Norwegian Women and Cancer (NOWAC) study and show how the complexity of NOWAC enables many beautiful new study designs. We discuss the challenges of implementing designs and analyzing data. Finally, ...

Biological data analysis is typically implemented using a deep pipeline that combines a wide array of tools and databases. These pipelines must scale to very large datasets, and consequently require parallel and distributed computing. It is therefore important to choose a hardware platform and underlying data management and processing systems well suited for processing large datasets. There are many ...

A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning) that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not ...

Kvik is an open-source system that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, ...

Machine learning approaches achieve high accuracy for text recognition and are therefore increasingly used for the transcription of handwritten historical sources. However, using machine learning in production requires a streamlined end-to-end pipeline that scales to the dataset size and a model that achieves high accuracy with few manual transcriptions. The correctness of the model results must ...

We describe our citizen science approach and technologies designed to introduce students in upper secondary schools to computational thinking and engineering. Using an Arduino microcontroller and low-cost sensors we have developed the air:bit, a programmable sensor kit that students build and program to collect air quality data. In our course, students develop their own research questions regarding ...

Increased levels of tumor-infiltrating lymphocytes (TILs) indicate favorable outcomes in many types of cancer. The manual quantification of immune cells is inaccurate and time-consuming for pathologists. Our aim is to leverage a computational solution to automatically quantify TILs in standard diagnostic hematoxylin and eosin-stained sections (H&E slides) from lung cancer patients. Our approach ...

We have attempted to reproduce the results in <i>Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs</i>, published in JAMA 2016; 316(22), using publicly available data sets. We re-implemented the main method in the original study since the source code is not available. The original study used non-public fundus images from EyePACS ...

A large up-to-date compendium of integrated genomic data is often required for biological data analysis. The compendium can be tens of terabytes in size, and must often be frequently updated with new experimental or meta-data. Manual compendium update is cumbersome, requires a lot of unnecessary computation, and it may result in errors or inconsistencies in the compendium. We propose a transparent ...