Services
Below tools are developed by the Brunak group over time to display and understand our research. These tools can help researchers and lay-people to explore the various aspects that in their own way play a significant part in understanding the links and linkages diseases, genes or chemical compounds.
The Danish Disease Trajectory Browser (DTB) is a tool for exploring almost 25 years of data from the Danish National Patient Register, http://dtb.cpr.ku.dk. In the data set comprising 7.2 million patients and 122 million admissions, users can identify diagnosis pairs with statistically significant directionality and combine them to linear disease trajectories. Users can search for one or more disease codes (ICD-10 classification) and explore disease progression patterns via an array of functionalities.
The tool is disease-agnostic across both rare and common diseases and is showcased by exploring multimorbidity in Down syndrome (ICD-10 code Q90) and hypertension (ICD-10 code I10). Finally, we show how search results can be customized and exported from the browser in a format of choice (i.e. JSON, PNG, JPEG and CSV).
BALDR is an automated pipeline for biomarker comparison and prioritization in the context of diabetes. BALDR includes protein, gene and disease data from major public repositories, text-mining data and human and mouse experimental data from the IMI2 RHAPSODY consortium. These data are provided as easy-to-read figures and tables enabling direct comparison of up to 20 biomarker candidates for diabetes.
The sequencing of 8,671 (5,418 women) individuals from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders in Danish individuals. https://danmac5.cpr.ku.dk/
We mapped the bioactivity of the ToxCast HTS assay data to a list of 207 AOPs maintained by OECD. After curation, 6,111 chemicals were identified as active at a non-cytotoxic concentration on 906 bioassays corresponding to molecular initiating events (MIEs) or key events (KEs) in AOPs. With this analysis, we have observed a variety of relevant connections between chemicals and AOP components.
The sAOP (stressor AOP) server is a resource for annotated AOPs (adverse outcome pathways) connected to toxic compounds from ToxCast. It is a compilation of more than 6000 chemical compounds annotated to the assay endpoints used for their detection, as well as more than 200 AOPs.
sAOP version 2: stressor Outcome Pathways tool. Search for toxic compounds related to AOPs.
Also check out version 1 of the stressor Adverse Outcome Pathway tool https://saop.cpr.ku.dk
Services from HeaDS
Health Data Science Sandbox
The Health Data Science Sandbox is a national project coordinated by the University of Copenhagen. The Sandbox is working with a network of health data science experts at five Danish universities to build training and research resources on academic supercomputers for students and researchers in Denmark.
The Sandbox contains training modules that pair shareable datasets from different health data domains with recommended analysis tools, pipelines, and learning materials/tutorials in a portable, containerized format.
The sandbox environment is hosted on Danish supercomputers Computerome and UCloud with open-source module materials hosted on GitHub (organization: hds-sandbox).
SUND DataLab
The SUND DataLab at HeaDS provides data science support for all research groups at SUND and oversees courses and workshops designed to upgrade the data science skills of biomedical researchers in-house at all seniority levels.
For more information about SUND Datalab, email datalab@sund.ku.dk
Further Services
We are developing further browsers based on our registry reaserch!
This includes a Service Registry Browser and a Prescription Registry Browser and Heritable Components of Multimorbidities and Disease Trajectories