Demonstrating EOSC-Nordic

Cecilie Maagaard Winther

Currently there are 10 use cases in the EOSC-Nordic project. All different and from 5 different fields. Learn more about the use cases and what they are demonstrating.

As an EU-project a lot of EOSC-Nordic happens on a governance and strategic level. Policies are being investigated, rules and guidelines thought out, surveys performed and webinars planned. But the project is also working closely with scientist trying to make or utilise what is to be the European Open Science Cloud.

In the EOSC-Nordic there are currently 10 use cases, demonstrators or pilot projects, as they are also called. It is 10 projects from 5 different scientific fields.

The idea of the use cases

The demonstrators have been selected to ensure representation from different disciplines and have been designed to foster interdisciplinary exchange. The use cases will demonstrate how to support cross border research collaboration, using the Nordic and Baltic countries as a testbed environment.

Furthermore, the approaches used in the demonstrators will leverage existing services and will be applicable in environments employing EOSC services outside of the Nordics.

In the Grant Agreement approved by the European Commission it states that:

“The ultimate objective is to demonstrate how thematic portals can concretely build on distributed data and computing resources offered by EOSC to scale out their storage and computing environment.”

The use cases in the EOSC-Nordic are the following:

Archaeology use case

Goal: The plan is to integrate the two national databases, the Danish “Fund og Fortidsminder” and the Norwegian “Askeladden”. By integrating the respective national databases, scientists can search both countries’ archaeological finds from the Viking age simultaneously.

“The Vikings were widespread with a widespread common material culture. So, if we find a tortoise brooch in the ground here in Denmark, well then, we can find something similar in Norway. It makes sense from the researcher’s point of view to have a common search interface,” explains Jens-Bjørn Riis Andresen, Associate professor at Aarhus University, School of Culture and Society at the Department of Archeology and Heritage Studies at the Moesgaard Museum in Aarhus.

He is collaborating with Senior Engineer Espen Uleberg from the University of Oslo, who is also Database Administrator at the Museum of Cultural History in Oslo and responsible for the Norwegian database.

The use case just reached its first milestone, as the other collaborating partner Deutsche Klimarechenzentrum (DKZ) in Hamburg have harvested all the data and made it available through the interdisciplinary service B2FIND. There are now 205.935 Danish archaeological data sets available via B2FIND, and they can now be found here.

Read more in the in-depth story about the use case here.

Natural Language Processing Lab for the Nordics

Natural Language Processing (NLP) is what happens when Siri, Alexa and Google Translate understand human or so-called “natural” language instead of formal or programming languages. NLP technology is a subdiscipline of artificial intelligence which means it is very data and computing heavy.

Goal: The NLP use case in EOSC-Nordic aims to make NLP research in Scandinavia more competitive in computational scale. Among other things the scientists are building a shared, uniform, virtual laboratory for large-scale experimental research in natural language processing.

“We want to enable our doctoral students and master’s students and also researchers on funded research projects to carry out computational experiments that are very resource-demanding. They need much bigger computers, than what are typically available through a local university’s computing infrastructure. And this use case in EOSC-Nordic is paving the road to make Nordic NLP researchers more efficient users of these large-scale national e-infrastructures,” says Stephan Oepen, professor of Machine Learning, Department of Informatics, University of Oslo.

He is working on this project along colleague Jörg Tiedemann, professor of Language Technology, from the University of Helsinki. Jointly, they represent the larger community, with university research groups in NLP in 4 countries that have collaborated for years.

The NLPL collaboration is comprised of Nordic research groups in NLP and the national e-infrastructure providers of Finland and Norway: Helsinki University (Finland), IT University Copenhagen (Denmark), University of Copenhagen (Denmark), University of Oslo (Norway), Turku University (Finland), and Uppsala University (Sweden) are the academic partners.

Read more about the NLPL collaboration here.

Climate 1 – Reproducible ecosystem models

Goal: This use case aims to integrate actual data and empirical knowledge in model development and operation so as to better take into account typical ecosystems only found at high latitudes, which are currently poorly represented.

Partners involved in the use case:

  • Lund University (Sweden)
  • University of Oslo (Norway)
  • Natural History Museum (Norway)

The use case wants to provide a virtual laboratory for developing and testing parameterizations of ecosystems and related processes to scientists whose expertise is not numerical modelling, and thereby increase the pace of model improvement from the bottom up. The case also aims to provide workflow management tools for operating these ecosystem models in a reproducible manner to realise their full potential without need for constant technical assistance. And also, to provide operational tools and infrastructure to facilitate the exploitation of ecosystem modelling for a wider audience and by non-specialists.

Climate 2 – FAIR Climate data for the Nordics

Goal: The goal is to provide FAIR climate data to all Nordic communities interested in climate mitigation and climate change impact assessment. This use case aims at serving NeIC NICEST-2 (the second phase of the Nordic Collaboration on e-Infrastructures for Earth System Modeling).

Partners involved in the use case:

  • National Supercomputing Centre, Sweden
  • Danish Meteorological Institute (DMI), Denmark
  • IT Center for Science (CSC), Finland
  • NORCE, Norway
  • The Norwegian Meteorological Institute (MetNo), Norway
  • University of Iceland (UoI), Iceland

Climate 3 – A community Virtual Laboratory for developing Climate diagnostics for the Nordics

Goal: This use case aims to share and develop Earth System Model Evaluation diagnostics and analysis using related data. This case also aims at serving NeIC NICEST-2.

Partners involved in the use case:

  • The Norwegian Meteorological Institute (MetNo), Norway
  • NORCE, Norway
  • University of Oslo, Norway
  • Finnish Meteorological Institute (FMI), Finland
  • Danish Meteorological Institute (DMI), Denmark
  • NERSC, Norway
  • University of Helsinki/INAR, Finland

The idea is to provide a platform for facilitating the development of a number of new tools. And with these new tools, researchers will be able to compare outputs from different climate models in the Nordic countries in order to identify deficiencies and develop strategies to improve a number of climate models.

Climate 4 – A community Virtual Laboratory for the development of machine-learning-based parameterizations and sub-models for clouds and land-surface processes in Earth System Models.

Goal: This case aims to improve existing parameterizations and prepare Earth System Models for future architectures by using machine learning.

Partners involved in the use case:

  • Finnish Meteorological Institute (FMI), Finland
  • University of Oslo, Norway
  • University of Helsinki, Finland
  • University of Iceland (UoI), Iceland

Learn more on the Climate use cases on GitHub.

Biodiversity 1

Goal: This use case aims to develop bioinformatics solutions for the Environmental DNA (eDNA) based species recovery and integrating these solutions with computing resources available through EOSC-Nordic.

This use case will present a list of modules and workflows designed to support submission of computations from PlutoF platform to a variety of scheduling systems in the Nordic HPC clusters.

Partners involved in the use case:

  • University of Tartu (Estonia)
  • University of Gothenburg (Sweden)
  • University of Copenhagen (Denmark)

Biodiversity 2

Goal: This use case aims to develop a data management platform for eco-genomic data, including machine-readable data management plans, extensive data provenance mechanisms, and an authentication/authorisation system.

The platform is based on the PlutoF data management system and will have functionality for interoperability with similar databases (e.g. GeoMe) and global data archives (e.g. OBIS, GBIF, ENA). The use case is currently set up in close collaboration with major European marine infrastructure networks linking a large user community from all across Europe to the system.

The use case will produce extensive documentation and training material for researchers in biodiversity, ecology, and conservation and organise regular training events for Nordic users during 2021-2023.

Partners involved in the use case:

  • University of Tartu (Estonia)
  • University of Gothenburg (Sweden)

Sensitive data 1 – Precision medicine

Goal: This use case aims to improve precision medicine and thereby reduce both overdiagnosis and underdiagnosis.

Precision medicine is to reduce both overdiagnosis and underdiagnosis. The data foundation will initially be the existing data. Subsequently, the project will be enriched by data for improvement of sub-classification of ischemic heart disease (IHD) and/or improved risk stratification within subgroups by imaging and omics data.

The use case aims to combine data from three countries – Denmark, Norway and Iceland.

Partners involved in the use case:

  • Computerome (Technical University of Denmark)
  • The Capitol Region of Denmark
  • Copenhagen University
  • University Center for Information Technology at University of Oslo
  • Swedish National Infrastructure for Computing (SNIC)
  • IT Center for Science (CSC)

Sensitive data 2 – Nordic Medication in Pregnancy and Childhood Cancer Consortium

Goal: The use case aims to investigate the association between maternal use of medications in pregnancy and the risk of childhood cancer, and determine which medications are safe to use in pregnancy when it comes to future risk of cancer in the child.

The study is about risk of childhood cancer after prenatal exposure to antibiotics and other medications – a Nordic registry-based study. The study will use data on pregnancy complications, redeemed prescriptions, and cancer diagnoses, all of which are considered sensitive data by law. Because childhood cancer is a very rare outcome, it is necessary to combine data from health registries in Denmark, Finland, Norway, and Sweden.

To comply with data protection laws, some previous Nordic collaborations have analysed the data separately in each country and combined the results using a meta-analysis approach. This use case hopes to avoid this, and to find a way for each country representative to share data to a single platform, where data can be analysed combined. The data should be accessible through a secure and encrypted VPN in a way that enables the PI in Norway and the collaborators in Denmark, Finland and Sweden to analyse data from all four countries as one data file.

Partners involved in the use case:

  • Swedish National Infrastructure for Computing (SNIC)
  • IT Center for Science (CSC)
  • Computerome (Technical University of Denmark)
  • University Center for Information Technology at University of Oslo

 

We will be following these use cases closely and write in-depth stories about each of them.