Ten simple rules for quick and dirty scientific programming
June 16, 2021 10:48 AM
“We argue that a quick and dirty style of programming is not necessarily bad: the quicker you code, the more scientific ideas you can potentially test and publish. However, if coding quickly means coding sloppily, then bugs, false conclusions, and article retractions may be the result. Furthermore, if your code becomes increasingly complex and messy over time, then adapting it to new tasks will be difficult, potentially stalling your research progress” says Geir Kjetil Sandve, Professor at the Centre for Bioinformatics.
The study was recently published in the popular ten simple rules series of PLOS Computational Biology and can be found here.
immuneML: a domain-tailored machine learning ecosystem to decipher adaptive immunity
June 16, 2021 10:32 AM
“We have developed a large software framework that provides a broad variety of machine learning modules for discovering patterns in immune data. It implements each step of the machine learning process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows” says Geir Kjetil Sandve, Professor at the Centre for Bioinformatics.
The study was recently made available on BioRxiv preprint server and can be found here.
The study has been a large team effort with contributions from national and international collaborators including the group of Victor Greiff, Associate professor at the Department of Immunology.
Fine-tuning epigenetic methods to create new knowledge from old samples
June 16, 2021 9:33 AM
“We have succeeded in extracting epigenetic information from scarce DNA from serum archived in the Janus Serum Biobank. This opens up new avenues for what serum banks can be used to achieve” says Trine B Rounge researcher at the Cancer Registry of Norway and Associate Professor at Centre for Bioinformatics.
The study, financed by Norwegian Cancer Society, was recently published in Clinical Epigenetics and can be found here.
In a collaborative national and international effort, the researchers conducted a study to test the feasibility of extracting more information from DNA from the Janus samples than was previously anticipated.
Insufficient knowledge of virus variants
Mar. 10, 2021 11:48 AM
The knowledge of corona virus variants in Norway has been insufficient, professor Eivind Hovig, director of the Centre for Bioinformatics, tells Norwegian media.
The latest publications from the Centre
Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer
Int J Cancer (in press)
Extensive bidirectional genetic overlap between bipolar disorder and cardiovascular disease phenotypes
Transl Psychiatry, 11 (1), 407
Identification of 22 susceptibility loci associated with testicular germ cell tumors
Nat Commun, 12 (1), 4487
Software developed at the centre
Software for extraction of DNA copy number motifs in cancer
Chimeraviz manages data from fusion gene finders and provides useful visualization tools.
Comparison of Adaptive Immune Receptor Repertoires
Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets
immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires
ScaR — a tool for sensitive detection of known fusion transcripts: establishing prevalence of fusions in testicular germ cell tumors
Highly-scalable and high-resolution amplicon clustering
A versatile open source tool for metagenomics
ELIXIR Norway is the Norwegian national node of ELIXIR, the pan-European infrastructure for biological information, supporting life science research and its translation to medicine, environment, the bioindustries and society. This organization is a virtual organization where the Center of Bioinformatics hosts the regional Oslo node. It participates to the national help-desk user support, and in that activity also collaborates and coordinates closely with the Helse Sør-Øst-funded Bioinformatics Core facility.