Projects
BIOcean5D is a major interdisciplinary project designed to better understand the impact of human activity on Europe’s seas and coastlines.
The overarching goal of BIOcean5D is to generate the data, knowledge, theory, monitoring and modelling tools necessary to sustainably measure, understand, value, and predict marine biodiversity across the five dimensions (5D) of space, time, and human environmental pressures, enabling ecosystem-based management and long-term preservation.
BIOcean5D unites major European centers in molecular and cell biology; marine biology; and sequencing, together with 31 partners from 11 countries, to build a unique suite of technologies, protocols, and models allowing holistic re-exploration of marine biodiversity, from viruses to mammals, from genomes to holobionts, across multiple spatial and temporal scales, stretching from pre-industrial history to today.
The main objectives of the project are:
To close the gap in knowledge on the structure, dynamics, and evolution of marine biodiversity within and across marine ecosystems by integrating existing biodiversity datasets and generating new biodiversity data across relevant taxonomic and spatio-temporal scales, environmental gradients, critical habitats, and taxa.
To understand the drivers and mechanisms of biodiversity changes and degradation, assess and predict marine ecosystem health, and provide quantitative eco-systemic tools for marine biodiversity policy implementation, by building a transdisciplinary theoretical and modelling framework informed by knowledge from Objective 1.
To develop and apply tools integrating the dynamics of functional biodiversity to measure the financial and non-financial value of marine life and ecosystem services and share new concepts of marine biodiversity services to ecosystems and societies through re-evaluation of conservation strategies and legal frameworks, as well as citizen engagement in marine science and literacy.
Our role in the project:
Within BiOceans5D, our team gathers historical and new data on marine plankton biogeography, biodiversity and ecosystem composition on regional to global scales. In collaboration with our international partners, and analyze this information using state-of-the-art machine learning and species distribution modeling algorithms. We analyze biodiversity across its major axes of variability: from the tropical ocean to the poles, from the surface to the ocean abyss, from the coast to the open ocean, across taxonomic groups and trophic levels and across the many different biodiversity metrics. We aim to provide consistent, quality controlled data sets on marine plankton diversity across data sources (including traditional microscopy and net counts, as well as new imaging data, eDNA and metagenomics), as well as to provide consistent, quality-controlled modeling pipelines to extrapolate and interpret these data sets.
People involved:
Alexandre Schickele
Stefanie Mayer
Fabio Benedetti
Corentin Clerc
Meike Vogt
Since October 2019, the pilot Blue-Cloud project combined both the interests of the European Open Science Cloud (EOSC), aiming to provide a virtual environment with open and seamless access to services for storage, management, analysis and re-use of research data, across borders and disciplines, and the blue research communities by developing a collaborative web-based environment providing simplified access to an unprecedented wealth of o multi-disciplinary datasets from observations, analytical services, and computing facilities essential for blue science.
Blue-Cloud 2026 aims at a further evolution of this pilot ecosystem into a Federated European Ecosystem to deliver FAIR & Open data and analytical services, instrumental for deepening research of oceans, EU seas, coastal & inland waters. It develops a thematic marine extension to EOSC for open web-based science, serving the needs of the EU Blue Economy, Marine Environment and Marine Knowledge agendas.
Over the course of 42 months starting in January 2023, Blue-Cloud 2026 will evolve the core services, integrating more blue analytical services, configuring more Virtual Labs, improving services for uptake of new data sets from a multitude of data originators (such as SeaDataNet, EurOBIS, Euro-Argo, ELIXIR-ENA, SOCAT, EcoTaxa, and ICOS-Ocean), and major e-infrastructures, namely EUDAT, D4Science, and WEkEO (CMEMS DIAS) and for discovery and access to their structured data collections.
Blue-Cloud 2026’s overall Objective is to expand the federated approach of Blue-Cloud, involving more aquatic data stakeholders, and interacting with EOSC developments, in support of the EU Green Deal, UN SDG, EU Destination Earth, and the EU Mission Starfish on healthy oceans, seas, coastal and inland waters, ultimately to provide a core data service for the Digital Twin of the Ocean.
Blue-Cloud Open Science Platform.
The current Blue-Cloud technical framework is extensible and open by design, constantly evolving according to the needs of the community, facilitating collaborative research and the uptake of Open Science principles, through a distinguished set of marine data services. The status of development of those services was at the core of different sessions during the GA:
Data Discovery & Access Service (DD&AS): An easy and FAIR service for discovering and retrieving multi-disciplinary data sets and products managed and provided by Blue Data Infrastructures. The federation facilitates sharing of datasets as input for analytical and visualisation services and applications, that are hosted and further developed in the Blue-Cloud Virtual Research Environment.
Virtual Research Environment (VRE): An Open Science platform for collaborative marine research, using a wide variety of datasets and analytical tools, complemented by generic services, such as sub-setting, pre-processing, harmonising, publishing and visualisation. The VRE hosts different Virtual Labs and is going to include thematic Workbenches, which users can access with existing credentials in EOSC, the European Open Science Cloud. Multi-disciplinary datasets retrieved from the Blue-Cloud DD&AS can be exploited in the VRE. All methods and services in the Catalogue are exchanged with the EOSC Portal Catalogue & Marketplace.
Thematic Virtual Labs (VLabs): where researchers work closely together with the Blue-Cloud 2026 technical team to describe Virtual Lab workflows and technical requirements, in order to implement them in the Blue-Cloud VRE and further test its capabilities on specific topics. The following Vlabs are available: Carbon-Plankton Dynamics, Global Fisheries Atlas, Coastal currents from observations, Integration of coastal ocean observations along Europe, Plankton Genomics, Marine Environmental Indicators, Aquaculture Monitor, Fish, a matter of scales and Zoo and Phytoplankton EOV products.
Workbenches for Essential Ocean Variables (EOVs): A seriesof data-intensive Workbenches for selected EOVs will be established where ocean and data scientists can implement efficient workflows that allow them to harmonise, validate and qualify large and diversein situ data sources, exploiting the blue analytical services available in the Blue-Cloud VRE. The following EOVs are available: Ecosystem-level EOVs, Eutrophication: chlorophyll, nutrients, oxygen and Physics: temperature & salinity.
Our role in the project:
Within BlueCloud2026, we lead the Ecosystems Level EOVs workbench (https://blue-cloud.org/workbenches-essential-ocean-variables-eovs/ecosystem-level-eovs). This workbench is an active collaboration between ETH Zurich, Sorbonne University and the EMBL-EBI European Molecular Biology Laboratory’s European Bioinformatics Institute).
The Workbench will improve the availability, quality and interoperability of large collections of plankton observations based on traditional counts, quantitative imaging and genomic methods available from the EMODnet/EurOBIS and ELIXIR data infrastructures.
It will develop a generic modelling workflow in Blue-Cloud 2026 to generate high-quality interpolated maps of the global distribution of these plankton entities. It will provide a sustainable workflow for production of ecosystem-level EOVs following clear QA/QC steps and according to best practices in habitat modelling.
People involved:
Alexandre Schickele
Corentin Clerc
Urs Hofmann Elizondo
Matthias Munnich
Meike Vogt
The Atlantic Ocean (AO) covers ~20% of Earth’s surface and contains ~25% of the global ocean volume. Both the circulation of water masses and the ecosystems of the AO play a key role in regulating Earth’s climate and sustain highly productive marine regions and fish stocks. The ensemble of microscopic organisms (the microbiome) that float in the AO waters, though invisible to the human eye, play a pivotal role in capturing and removing CO2 from the atmosphere and in supporting the quantity of biomass available to fishes. The mean annual value added by the Atlantic maritime economy was estimated to exceed 400 billion dollars over the last 20 years, and this value is expected to continuously increase in the future. However, the state of AO ecosystems and the services provided by the microbiome are also increasingly threatened by human activities and global climate change. In a context of ever-expanding human impacts on marine resources and rapid climatic changes (e.g. changes in temperature, ocean circulation, ocean acidification, coastal erosion and the input of harmful nutrients, pollutants and microplastics), one of the greatest challenges of our time is to understand and preserve existing ecosystem services and to ensure the good environmental status of ecosystems.
Within this context, the AtlantECO H2020 project aims to develop and apply a novel unifying framework for providing knowledge-based resources to design policies, support decisions making and engage with citizens to encourage responsible behavior to manage AO system. AtlantECO revolves around four main objectives:
1. To assess the status of ecosystem structures, functions, health and services at various scales and to provide high quality gridded data products and maps.
2. To enhance knowledge and innovate by adopting standard optical and genetic observations protocols, cutting-edge network analysis methods, and better parameterizations of connectivity and biogeochemical models.
3. To assess drivers and stressors of change and forecast their impact on tipping points and recovery of ecosystem structures, functions and services, and to develop eco-socio-economic models to predict their future states.
4. To share and use capacity and knowledge across the four continents bordering the AO ensuring a seamless engagement between science, industry, policy, and society.
Within the framework of of the first objective above, members of the UP group co-lead AtlantECO’s WP2 « Marine ecosystem structure and function » (Dr. Meike Vogt, Dr. Fabio Benedetti and Dominic Ericsson). ETH UP is responsible for assembling the most extensive 3D biogeography (i.e. mapping) of the biodiversity and abundance of the microbiome at the scale of the AO. In collaboration with 18 international partner institutes, we engage in the following main tasks:
1. To assemble and map existing and new geo-referenced observations about the microbiome, plastics, the plastisphere (i.e. the microbiome interacting with the floating plastics debris) and carbon fluxes.
2. To assemble and map essential ocean variables and indicators of ecosystem services such as biodiversity, bioresources, productivity, food provision and climate support services.
3. To comprehensibly assess the status and functioning of the Atlantic Ocean ecosystem.
Ultimately, the diverse range of quality-controlled and spatially-explicit data produced by our team and collaborators will serve as a basis for analyses carried out by all 35 partnering scientific institutes.
Related links
external page call_made European Commission CORDIS EntryKey publications
Benedetti, F., Vogt, M., Elizondo, U. H., Righetti, D., Zimmermann, N. E., & Gruber, N. (2021). Major restructuring of marine plankton assemblages under global warming. Nature Communications, 12(1), 5226. doi:10.1038/s41467-021-25385-x
EERIE (European Eddy Rich Earth System Models) is a Horizon Europe project that runs from 2023 to 2026. The aim of the project is to explore and quantify the role of mesoscale ocean features in the climate system from seasonal to centennial time scales. To achieve this, a new generation of Earth System Models (ESMs) is being developed that are capable of explicitly representing ocean mesoscale features, like eddies, fronts, and jets. Such simulations will help to improve our understanding of climate variability, tipping points, and climate extremes and contribute to national and international climate change assessments such as IPCC.
(external page https://eerie-project.eu/)
EXCLAIM (EXtreme scale Computing and data platform for cLoud-resolving weAther and clImate Modeling), is a 6 year open ETH project (2021-2027) that aims to develop an ICON-model based infrastructure that is capable of running kilometer-scale climate simulations at both regional and global scales. Learn more about our vision.
The work is conducted in a highly collaborative effort that brings together computer scientists with data and domain experts
EXCLAIM core team
EXCLAIM principle investigators
EXCLAIM partners and international collaborations
EXCLAIM requires using innovative coding concepts and exploiting the next generation of supercomputer architectures and the power of novel hardware systems including accelerators such as Graphics Processing Units (GPU). Check out the implementation plan.