Blue-Cloud

Part of EU Open Research Repository
Published June 30, 2026 | Version 1
Project deliverable Open

Blue-Cloud 2026 - D3.3 Workbenches and tools (notebooks model, containers with instructions)

Authors/Creators

  • 1. ROR icon Istituto Nazionale di Geofisica e Vulcanologia
  • 2. EDMO icon Ifremer Head Office
  • 3. EDMO icon Pokapok
  • 4. ROR icon Hellenic Centre for Marine Research
  • 5. EDMO icon National Oceanography Centre (Liverpool)
  • 6. EDMO icon Marine Information Service
  • 7. ROR icon Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung
  • 8. EDMO icon Oceanscope
  • 9. ROR icon National Institute of Oceanography and Applied Geophysics
  • 10. ROR icon Swedish Meteorological and Hydrological Institute
  • 11. ETHZ
  • 12. ROR icon Sorbonne Université
  • 13. ROR icon European Bioinformatics Institute

Description

This deliverable encompasses the workflows, tools and user documentation for the three analytical Workbenches developed within Work Package 3 of the Blue-Cloud 2026 project.

These Workbenches implement cloud-based analysis pipelines that enable ocean scientists, data managers and modellers - among others - to produce harmonised, high-quality Essential Ocean Variable (EOV) and Essential Biodiversity Variable (EBV) datasets more easily and rapidly, overcoming the fragmentation of marine data across heterogeneous infrastructures. They leverage on the Blue-Cloud Virtual Research Environment and cloud-computing platform powered by D4Science, and can be customised to the user's needs.

The Physics Workbench (https://blue-cloud.d4science.org/web/physics-workbench) enables users to integrate temperature and salinity data from four infrastructures – SeaDataNet, Copernicus Marine Service (CORA product), EuroARGO and World Ocean Database – through a workflow combining semantic harmonisation, quality control and duplicate detection, delivering added-value EOV dataset that can be used in ocean reanalysis, climate normals, ocean monitoring indicators, and AI-driven applications.

The Eutrophication Workbench (https://blue-cloud.d4science.org/web/eutrophication-workbench) provides a cloud-based environment to generate harmonised, complete, deduplicated EOV collection for chlorophyll-a, nutrients, and dissolved oxygen, federating data from Copernicus Marine Service, EMODNet Chemistry and the World Ocean Database, in line with GOOS recommendations. Both share a common technical foundation based on the BEACON datalake and semantic harmonisation, as well as common tools (CW Duplicates Detection tool for duplicate handling, WebODV for data exploration and visualization, FileForge for data conversion and annotation), with the exception of the MinMax Alert Tools used for additional quality control by the Physics Workbench only.

The Ecosystem Workbench (https://blue-cloud.d4science.org/web/ecosystem-workbench) aims to improve the availability, quality and interoperability of marine plankton observations to diagnose EOVs and EBVs related to plankton biomass and diversity. It leverages the CEPHALOPOD species habitat modelling pipeline that combines automated data processing, machine learning and quality control to produce global spatial distribution estimates from heterogeneous observation types from major biological data initiatives such as GBIF, OBIS, AtlantECO, EcoTaxa, ELIXIR (MGnify). Outputs are accessible interactively through the Cephaloview application.

All three Workbenches, their notebooks and components are fully documented and designed to ensure the reproducibility of their results. They are open to external users, available for reuse under open-source licenses through the Blue-Cloud VRE and catalogue (https://blue-cloud.d4science.org/catalogue-bluecloud-cloud) and open repositories (Git, Zenodo and Software Heritage). Their results are planned for integration into the European Open Science Cloud (EOSC) and the European Digital Twin Ocean (EDITO) through the EOSC Node European Digital Twin Ocean.

Files

Blue-Cloud2026_D3.3_Workbenches_and_tools.pdf

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Additional details

Related works

Is compiled by
https://data.d4science.org/ctlg/Blue-Cloud2026Project/blue-cloud_2026_-_d3_3_workbenches_and_tools_notebooks_model_containers_with_instructions_ (URL)

Funding

European Commission
Blue-Cloud 2026 - A federated European FAIR and Open Research Ecosystem for oceans, seas, coastal and inland waters 101094227