Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities

Informations projet

BioDT

N° de convention de subvention: 101057437

DOI

10.3030/101057437

Projet clôturé

Date de signature de la CE 31 Mai 2022

Date de début 1 Juin 2022

Date de fin 31 Mai 2025

Financé au titre de

• Research infrastructures

Coût total

€ 11 059 061,00

Contribution de l’UE

€ 11 059 061,00

Coordonné par

CSC-TIETEEN TIETOTEKNIIKAN KESKUS OY
Finland

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (13)

Productisation roadmap

Roadmap describes the steps needed for productisation and large-scale adaptation of the Digital Twin Advanced Technical Platform. The roadmap will be aligned with the developments of the European Open Science Cloud, as well as the activities under the EuroHPC joint initiative.

Recommendations towards connecting multiple twins

This report will provide an overview of lessons learned and recommendations towards connecting multiple twins initiatives (DestinE, Ocean, EOSC, EUDS, etc) that can be adopted by RIs and other work packages towards the establishment of a Special Interest Group.

Data Management Plan

The DMP will evolve during the lifetime of the project in order to present the status of the project's reflections on data management.

Report on model upscaling approaches

Report on approaches implemented for model upscaling. Description of relative performance improvements gained through executing the upscaled models on LUMI. Updated model source code will be released through a public repository.

Plan for dissemination & exploitation including communication activities

This report presents the plan for targeted engagement and all outreach exploitation and communication strategies

Architecture and implementation plan

Describes the architecture for the Digital Twin platform core components and shared services Documents information security practices and more detailed implementation plan

Digital Twins Ecosystem Interest Group Manifesto

This report will provide an analysis and roadmap on how the various digital twins initiatives can be connected to each other for maximum impact and coverage.

Final plan dissemination & exploitation including communication activities

Outlines stakeholder groups and targeted engagement activities & achievements.

Report on DT predictive capacity

Report on the predictive capacity of the DT in relation to its real-life counterpart, based on validation test results. The report will focus on the performance of the DT as a next-generation tool for aiding decision support and policy development within the field of biodiversity research.

Report of results on applying models, data, and data streams covering the use cases

BioDT modelling outcomes are developed, tested, prototyped and applied, with workshops / training events, across the eight use cases covering species response to environmental change, genetically detected biodiversity, threatened and invasive species, as well as species interactions and planetary well-being.

First stage community platform integration report

The initial integration process will be defined and related tools will be analysed based on the requirements, architecture development, and data and models development.

Report on the availability of consolidated, improved, fit for use data streams, data model availability, improvement, and application

A variety of heterogeneous streams of biodiversity data from a range of sources and scales, as well as accompanying abiotic data is secured and developed, through interactions with RIs and expert communities, to ensure the fuelling the BioDT functions with FAIR attribution and data citations.

RI skills mapping & Good Practices and training report

Map the skills & Good Practices identified and developed in other work packages throughout the project and report of the training activities, including a dedicated report on the Summer School.

Demonstrators, pilots, prototypes (6)

Release of end-user features for simulations, predictions and biomonitoring

Release of end-user features for interactive use of the DT, focusing on simulation and prediction tasks related to the use cases. Description of features for producing data summaries and online visualisations (e.g. maps) for now-casting optimal data collection locations for citizen scientists.

Pilot Service to open up FAIR semantic mappings for FDO

This deliverable will produce a pilot service focused FAIR semantic mappings for FAIR Digital Objects (FDOs). FAIR principles and FDOs provide a foundation to organise multidisciplinary heterogeneous data by improving machine-actionability, interoperability and reusability. Semantic mappings plays an important role here. This deliverable will provide a service to open up the matching results for subsequent quality evaluation, FAIR compliant reuse as well as estimation and quantification of semantic similarity. The mappings will be provided through various services and tools such as OxO (EBI) and EcoPortal (LifeWatch ERIC).

Pipeline release and validation

Description and release of pipelines and building blocks for model fitting and validation, prediction and simulation tasks, and data visualization. These will cover each of the use cases and methods being addressed, with validation of the pipelines based on small-scale pilot analyses.

Pilot integration of workflows and data products organised through FDO with common community workflows and data products used within the RIs

This deliverable focuses on pilot integration of workflows and data products organised through FAIR Digital Objects with common community workflows and data products used within the infrastructures.

Final community platform integration report

Demonstration of the Digital Twin integration with external community environments.

Software for digital twin advanced technical platform

Components and integrations that form the technical platform are released with an open source license to make it widely available, support sustainability of the platform and adhere with the principles of open science.

Publications

Other (61)

"Presentation ""Digital Twin Empowered Biodiversity Conservation: Sustainable Forest Management"", presented at the World Biodiversity Forum 2024"

Auteurs: Afsar B, Versluijs M, Eyvindson K, Ovaskainen O
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15623398

"Abstract ""Digital twin enabled forest management with multiobjective optimization"", IBFRA 2023: Climate resilient and sustainable forest management"

Auteurs: Afsar B, Eyvindson K, Versluijs M, Ovaskainen O
Publié dans: IBFRA Conference 2023: Book of abstracts, Numéro 77, 2023, ISSN 2342-7639
Éditeur: Natural Resources Institute Finland (Luke)

"Abstract ""Can hive weight from monitoring campaigns (TRACHTNET) be predicted by land cover products and weather data?"", 71. Jahrestagung der Arbeitsgemeinschaft der Institute für Bienenforschung e.V."

Auteurs: Groeneveld J, Wendt A, Grimm V
Publié dans: Book of Abstracts of 71. Jahrestagung der Arbeitsgemeinschaft der Institute für Bienenforschung e.V., 2024
Éditeur: Association of the German Bee Research Institutes

"Abstract ""Dataspace Integration for Agrobiodiversity Digital Twins with RO-Crate"", SPNHC-TDWG 2024"

Auteurs: Weiland C, Grieb J, Bauer D, Chala D, Kusch E, Andrew C, Endresen D
Publié dans: Biodiversity Information Science and Standards, Numéro 8, 2024, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.8.134479

Survey and Monitoring Data Quick-Start Guide A how-to for updating a Darwin Core dataset using the Humboldt Extension

Auteurs: Ingenloff K
Publié dans: 2025
Éditeur: GBIF Secretariat: Copenhagen
DOI: 10.35035/DOC-7T3P-VE38

"Presentation ""Adapting the Digital Twin Paradigm to the Requirements of Biodiversity"", presented at the World Biodiversity Forum 2024"

Auteurs: Nikolova N & Brewster C
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15601987

"Abstract ""Mapping.bio: Piloting FAIR semantic mappings for biodiversity digital twins"", TDWG 2023"

Auteurs: Wolodkin A, Weiland C, Grieb J 
Publié dans: Biodiversity Information Science and Standards , Numéro 7, 2023, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.7.111979

"Poster ""Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting"", 1st International Conference on FAIR Digital Objects"

Auteurs: Soiland-Reyes S, Sefton P, Castro LJ, Coppens F, Garijo D, Leo S, Portier M, Groth P, Goble C
Publié dans: 1st International Conference on FAIR Digital Objects, Numéro 1ST, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7245315

Guide for publishing biological survey data to GBIF

Auteurs: Ingenloff K, Svenningsen C, Earl C, Shimabukuro PHF, Sica Y, Gan Y-M, Kachian ZR, Brenton P, Hochachka W, Wieczorek J, Stevenson R, Kazem A, Baskauf S, Zermoglio PF, Bloom D, Rodrigues A, Gamboa Martínez J & Schigel D.
Publié dans: 2025
Éditeur: GBIF Secretariat: Copenhagen
DOI: 10.35035/DOC-YNVS-EH84

"Presentation ""TwinEco: A unified framework for dynamic data-driven digital twins in ecology"", presentation of the TwinEco paper at the World Biodiversity Forum 2024"

Auteurs: Khan T
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15575560

"Abstract ""Die Honigbiene in Agrarlandschaften: Simulationen mit dem Model BEEHAVE"", Bienen und Landwirtschaft: Strategiekonferen 2024"

Auteurs: Groeneveld J, Grimm V
Publié dans: Book of Abstracts of Strategiekonferenz der Deutschen Agrarforschungsallianz, 2024
Éditeur: Deutsche Agrarforschungsallianz (DAFA)

"Presentation ""Building diverse collections using RO-Crate"", ELIXIR All Hands 2023"

Auteurs: Soiland-Reyes S, Goble C
Publié dans: ELIXIR All Hands 2023, 2023
Éditeur: F1000Research
DOI: 10.7490/f1000research.1119466.1

"Abstract ""Data Standards and Interoperability Challenges for Biodiversity Digital Twin: A novel and transformative approach to biodiversity research and application"", TDWG 2023"

Auteurs: Islam S, Koivula H, Endresen D, Kusch E, Schigel D, Addink W 
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.7.112373

"Abstract ""The Importance of Interoperability in European Research Infrastructures"", ACCC-FASN Science Conference 2023"

Auteurs: Souza A, Rasilo T, Bäck J 
Publié dans: Report Series Aerosol Science, Abstract Book of the ACCC-FASN Science Conference 2023, Numéro 271, 2023, ISSN 2814-4236
Éditeur: The Finnish Association for Aerosol Research (FAAR)

"Poster ""Biodiversity Digital Twin: Implementation Status and Extension Opportunities"", 2nd Destination Earth User eXchange"

Auteurs: Harrison J, Aalto T, Oostervink N, Geenen T
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.12722280

"Poster ""eLTER and BioDT: Creating Interactive Digital Twins with R Shiny"", presented at eLTER Consortia meeting, 3-7 June 2024"

Auteurs: Souza A., Sara-aho K, Rolph S, Salamon O, Martinovič T
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15269900

"Abstract ""Connecting people and nature to ensure resilient landscapes"", BES Symposium 2024"

Auteurs: Dick J, Rolph S, Andrews C
Publié dans: Resilient Landscapes for People, Nature Climate. BES Symposium Book of Abstracts, 2024
Éditeur: British Ecological Society (BES)

"Poster ""Biodiversity Digital Twin: Advancing predictive biodiversity modelling"", 3rd Destination Earth User eXchange"

Auteurs: Aalto T, Sara-aho K, Zuquim G, Pleiter D, Geenen T
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.13938825

BioDT poster at ISC High Performance 2023

Auteurs: Martinovic T, Drago F
Publié dans: ISC High Performance 2023, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8033683

"Abstract ""Transforming Knowledge into Practice: Science, Technology and Innovation in Support of the UN SDGs"", Science Summit 2024"

Auteurs: Arvanitidis C, Barov B, Basset A, Deneudt K, González Ferreiro M, Drago F, Huertas Olivares C, Kirrane D, Koureas D, Manola N, Mietchen D, Pade N, Penev L, Zuquim G, Ioannidis Y
Publié dans: Reseach Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft

"Presentation ""Designing Dynamic Data-Driven Digital Twin Systems in Ecology"" from the same-titled workshop at ECEM 2023"

Auteurs: Khan T
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8313904

Metabarcoding Data Toolkit – user guide

Auteurs: Frøslev T
Publié dans: 2025
Éditeur: GBIF Secretariat: Copenhagen
DOI: 10.35035/DOC-WKPC-M352

"Presentation ""Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities"", presented at the Netherlands Biodiversity Information Facility (NLBIF) Day 2023"

Auteurs: Islam S
Publié dans: Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8144429

"Abstract ""Mobilising Long-Term Natural Environment and Biodiversity Data and Exposing it for Federated, Semantic Queries"", TDWG 2023"

Auteurs: Koivula H, Wohner C, Magagna B, d`Aragona P, Oggioni A 
Publié dans: Biodiversity Information Science and Standards , Numéro 7, 2023, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.7.112221

"Presentation of the Crop Wild Relative use case: ""Crop wild relatives Digital Twin: where data flow meets computation to revolutionize agricultural research"", Living Norway Colloquium 2023"

Auteurs: Chala, D
Publié dans: Living Norway Colloquium 2023, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8040132

"Abstract of conference paper ""Digital Twin and Foundation Models: A New Frontier"", 16th International Conference on Agents and Artificial Intelligence (ICAART 2024)"

Auteurs: Trantas A, Pileggi, P
Publié dans: ICAART 2024 Final Program and Book of Abstracts, 2024
Éditeur: SCITEPRESS - Science and Technology Publications

"Presentation ""Updating Linked Data practices for FAIR Digital Object principles"", 1st International Conference on FAIR Digital Objects"

Auteurs: Soiland-Reyes S, Castro LJ, Garijo D, Portier M, Goble C, Groth P
Publié dans: 1st International Conference on FAIR Digital Objects, Numéro 1ST, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7256428

"Abstract and presentation ""Monitoring and protecting biodiversity with Digital Twins"", ECEM 2023"

Auteurs: Taubert F, De Bakke M, Banitz T, Grimm V, Groeneveld J, Ovaskainen O
Publié dans: ECEM 2023 Book of Abstracts, 2023
Éditeur: Helmholtz Centre for Environmental Research GmbH (UFZ)
DOI: 10.5281/ZENODO.15553252

"Presentation ""The Digital Twin Paradigm for Biodiversity Research Data"" at FAIR Digital Objects Forum lecture Concept of Digital Twins /Surrogates"

Auteurs: Islam S
Publié dans: FAIR Digital Objects Forum lecture Concept of Digital Twins /Surrogate, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7852889

Biodiversity data standards for the organization and dissemination of complex research projects and digital twins: a guide

Auteurs: Andrew C, Islam S, Weiland C, Endresen D
Publié dans: 2024, ISSN 2331-8422
Éditeur: ArXiv / Cornell University
DOI: 10.48550/ARXIV.2405.19857

"Poster ""The Importance of Interoperability in European Research Infrastructures"", ACCC-FASN Science Conference 2023"

Auteurs: Souza A, Rasilo T, Bäck J
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.10203382

"Poster ""FAIR Dataspace Integration for Agrobiodiversity Digital Twins"", 3rd Destination Earth User eXchange"

Auteurs: Bauer, D., Kusch, E., Weiland, C., Grieb, J., Chala, D., & Endresen, D. 
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.13928655

"Poster ""Upscaling Biodiversity Modelling from Laptops to Supercomputers"" presented at the 2025 Nordic-RSE conference"

Auteurs: Rossi T & Martinovič T 
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15536282

"Poster ""Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate"", ELIXIR All Hands 2023"

Auteurs: Leo S, Rodríguez-Navas L, Fernández JM, De Geest P, Pireddu L, Crusoe MR, Garijo D, Colonnelli I, Sirvent R, Soiland-Reyes S
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/ZENODO.8004793

"Abstract ""Towards a digital twin to simulate bee health for Germany"", High Performance Computing Conference 2023"

Auteurs: Groeneveld J, Krebs J, Martinovic T, Rossi T, Wendt A, Grimm V
Publié dans: NHR Conference '23 Book of Abstracts, 2023
Éditeur: National High Performance Computing (NHR Alliance)

"Presentation ""How can we better understand the impact of global change on bees using mechanistic simulation models and monitoring campaigns?"" presented at the GfÖ 2024 Annual Meeting"

Auteurs: Groeneveld, J.
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15409988

"Poster ""Digital twin linking cultural ecosystem services of recreational potential and biodiversity in the Cairngorms National Park"", workshop Assessing and Preserving Soundscapes in National Parks"

Auteurs: Dick J, Rolph S, Andrews C, Watkins J
Publié dans: workshop at Cairngorms National Park, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8038537

"Presentation ""Challenges in Data and Model Integration for Biodiversity Digital Twin Applications"", presented at the ELIXIR Biodiversity Community (monthly meeting), 23 October 2024 "

Auteurs: Islam S
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.13982672

"Presentation ""Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities"", presented at eLTER Consortia meeting 2024"

Auteurs: Zuquim G
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.12166859

"Presentation ""Overview of FAIR data publishing with bioschemas & RO-Crate"", ELIXIR All Hands 2023"

Auteurs: Soiland-Reyes S, Castro LJ
Publié dans: Overview of FAIR data publishing with bioschemas & RO-Crate, 2023
Éditeur: F1000 Research
DOI: 10.7490/f1000research.1119459.1

"Preprint ""Accelerating joint species distribution modeling with Hmsc-HPC: A 1000x faster GPU deployment"""

Auteurs: Rahman A, Tikhonov G, Oksanen J, Rossi T, Ovaskainen O
Publié dans: 2024, ISSN 2692-8205
Éditeur: BioRxiv / Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.13.580046

"Presentation ""A digital twin linking recreational potential and biodiversity in the Cairngorms National Park"", workshop Assessing and Preserving Soundscapes in National Parks"

Auteurs: Dick J, Andrews C, Rolph S, Watkins J
Publié dans: A digital twin linking recreational potential and biodiversity in the Cairngorms National Park, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8038203

"Presentation ""Digitalisation for Sustainable Nature"", presented for the European Environment Agency"

Auteurs: Broekhuijsen, J
Publié dans: Digitalisation for Sustainable Nature, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.8135415

"Poster ""Simulating the effect of landscape structure and land use change on honey bee vitality for Germany"", 2023 Annual meeting of the Ecological Society (GfÖ)"

Auteurs: Groeneveld J, Krebs J, Martinovic T, Rossi T, Wendt A, Grimm V
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.12580924

BioDT poster at EuroHPC Summit 2023

Auteurs: Drago, Federico; Pleiter, Dirk; Martinovic, Tomas
Publié dans: EuroHPC 2023, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7754745

"Presentation ""A Digital Twin of grassland ecosystems"", presented at the World Biodiversity Forum 2024"

Auteurs: Taubert F, Banitz T, Rossi T, Wohner C, Venier S, Martinovič T, Khan T, Lopez Gordillo, J
Publié dans: 2025
Éditeur: Zenodo

"Abstract ""eLTER and its role of providing in-situ data to large scale research projects for modelling biodiversity dynamics"", EGU General Assembly 2024"

Auteurs: Wohner C, Oggioni A, Tagliolato P, Taubert F, Banitz T, Venier S, Trembath P and Peterseil J
Publié dans: 2024
Éditeur: European Geosciences Union (EGU)
DOI: 10.5194/egusphere-egu24-1555

"Poster ""Sharing data as machine-actionable objects using RO-Crate, Bioschemas and Signposting"", ELIXIR All Hands 2023"

Auteurs: Soiland-Reyes S, Leo S, Castro LJ, Sefton P, Goble C
Publié dans: ELIXIR, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8004796

"Abstract ""Bridging Data Standards and FAIR Principles in Biodiversity Digital Twinning: Prototyping, Challenges, Lessons Learned, and Future Plans"", SPNHC-TDWG 2024 Joint Conference"

Auteurs: Islam S, Lopez Gordillo J, Endresen D, Andrew C 
Publié dans: Biodiversity Information Science and Standards, Numéro 8, 2024, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.8.133089

"Presentation ""Show and Tell: BioDT and DISSCo Perspective"" at FAIR-IMPACT Workshop: Why Mappings Matter and how to make them FAIR?"

Auteurs: Le Franc Y,  Harmse H, De Santis L, Jeffery K, Matentzoglu N, Weiland C
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/ZENODO.8162873

"Abstract ""Enhancing data integration with existing FAIR enabling resources: a case for using the Darwin Core and its extensions to integrate eLTER biosphere data with other biodiversity data"", eLTER Science Conference 2025"

Auteurs: Ingenloff K
Publié dans: ARPHA Conference Abstracts, Numéro 8, 2025, ISSN 2603-3925
Éditeur: Pensoft
DOI: 10.3897/ACA.8.E151692

"Presentation ""Sharing research artefacts as FAIR Digital Objects using RO-Crate"", presented at Brookhaven National Laboratory"

Auteurs: Goble C, Soiland-Reyes S
Publié dans: Sharing research artefacts as FAIR Digital Objects using RO-Crate, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7915818

"Presentation materials ""Building diverse FDO Collections using RO-Crate: An overview of the RO-Crate concept and its implementations"" from FAIR Digital Object Forum workshop Defining FDO Collections"

Auteurs: Soiland-Reyes S, Goble C
Publié dans: Building diverse FDO Collections using RO-Crate: An overview of the RO-Crate concept and its implementations, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7915603

"Abstract ""Building Biodiversity Digital Twins"", SPNHC-TDWG 2024"

Auteurs: Schigel D
Publié dans: Biodiversity Information Science and Standards, Numéro 8, 2024, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.8.139100

"Poster ""Applying the Digital Twin Concept to Ecological Reality: Challenges and Lessons Learned"", BES Annual Meeting 2024"

Auteurs: Rolph, S., Andrews, C., Carbone, D., Gordillo, J. L., Martinovič, T., Oostervink, N., Pleiter, D., Sara-aho, K., Wohner, C., Williams, M., Tigli, M., Marsh Rossney, J., Watkins, J., & Dick, J.
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/ZENODO.14331464

"Abstract ""Modelling Research Expeditions in Wikidata: Best Practice for Standardisation and Contextualisation"", TDWG 2023"

Auteurs: von Mering S, Braun PJ-C, Cubey RWN, Groom Q, Haston EM, Hendriksen A, Johaadien R, Leachman S, Marsden L, Rainer H, Santos J, Endresen D
Publié dans: Biodiversity Information Science and Standards , Numéro 7, 2023, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/biss.7.111427

"Abstract ""How do honeybees respond to landscape structure and other stressors?"", ECEM 2023"

Auteurs: Groeneveld J, Wendt A, Krebs J, Grimm V
Publié dans: ECEM 2023 Book of Abstracts, 2023
Éditeur: Helmholtz Centre for Environmental Research GmbH (UFZ)

"Presentation ""Utilizing digital twins for crop wild relatives: advancing food security and conservation efforts"", Nordic stakeholder workshop Long-term Conservation and Access to Nordic Crop Wild Relatives"

Auteurs: Chala, D
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.10055794 

"Abstract ""From data pipelines to FAIR data infrastructures: A vision for the new horizons of bio- and geodiversity data for scientific research"", 1st International Conference on FAIR Digital Objects"

Auteurs: Islam S, Weiland C, Addink W
Publié dans: Research Ideas and Outcomes, Numéro 8, 2022, ISSN 2367-7163
Éditeur: Pensoft Publishers
DOI: 10.3897/RIO.8.E93816

"Presentation ""FAIR Data and Models in Biodiversity Digital Twins"", presented at the World Biodiversity Forum 2024"

Auteurs: Islam S
Publié dans: 2025
Éditeur: Zenodo
DOI: 10.5281/ZENODO.15553776

"Abstract ""Graphical User Interface for Biodiversity Digital Twins: Data Challenges"", SPNHC-TDWG 2024 Joint Conference"

Auteurs: Martinovič T, Sara-aho K, Salamon O, Rolph S, Souza A
Publié dans: Biodiversity Information Science and Standards, Numéro 8, 2024, ISSN 2535-0897
Éditeur: Pensoft
DOI: 10.3897/BISS.8.135092

Peer reviewed articles (25)

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Auteurs: Soiland-Reyes S, Goble C, Groth P.
Publié dans: PeerJ Comput Sci, 2024, ISSN 2376-5992
Éditeur: San Diego CA: PeerJ Inc
DOI: 10.48550/arXiv.2306.07436

Prototype biodiversity digital twin: Forest biodiversity dynamics

Auteurs: Afsar B, Eyvindson K, Rossi T, Versluijs M, Ovaskainen O
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e125086

rdata: A Python library for R datasets

Auteurs: Carlos Ramos-Carreño, Tuomas Rossi
Publié dans: Journal of Open Source Software, Numéro 9, 2024, ISSN 2475-9066
Éditeur: Journal of Open Source Software
DOI: 10.21105/JOSS.07540

High-resolution spatiotemporal forecasting of the European crane migration

Auteurs: De Koning K, Nilsson L, Månsson J, Ovaskainen O, Kranstauber B, Arp M, Schakel JK
Publié dans: Ecological Modelling, Numéro 498, 2024, ISSN 0304-3800
Éditeur: Elsevier BV
DOI: 10.1016/j.ecolmodel.2024.110884

Prototype biodiversity digital twin: honey bees in agricultural landscapes

Auteurs: Groeneveld V, Martinovic T, Rossi T, Salamon O, Sara-aho K, Grimm V
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e125167

Expanding the Scope of the Bumblebee Model BEE-STEWARD: A Simple Foraging Module Facilitates the Parameterization

Auteurs: Luttermann M, Prestele R, Grimm V, Groeneveld J
Publié dans: Ecology and Evolution, Numéro 15, 2025, ISSN 2045-7758
Éditeur: John Wiley and Sons
DOI: 10.1002/ECE3.71468

Prototype Digital Twin: Recreation and biodiversity cultural ecosystem services

Auteurs: Rolph S, Andrews C, Carbone D, Lopez Gordillo J, Martinovič T, Oostervink N, Pleiter D, Sara-aho K, Watkins J, Wohner C, Bolton W, Dick J
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/ARPHAPREPRINTS.E125515

A Mobile Application–Based Citizen Science Product to Compile Bird Observations

Auteurs: Ossi Nokelainen, Patrik Lauha, Sebastian Andrejeff, Jari Hänninen, Jasmin Inkinen, Aleksi Kallio, Harry J. Lehto, Marko Mutanen, Riku Paavola, Pauliina Schiestl-Aalto, Panu Somervuo, Janne Sundell, Jussi Talaskivi, Mikko Vallinmäki, Aurélie Vancraeyenest, Ari Lehtiö, Otso Ovaskainen
Publié dans: Citizen Science: Theory and Practice, Numéro 9, 2024, ISSN 2057-4991
Éditeur: Ubiquity Press, Ltd.
DOI: 10.5334/CSTP.710

Digital twins: dynamic model-data fusion for ecology

Auteurs: de Koning K, Broekhuijsen J, Kühn I, Ovaskainen O, Taubert F, Endresen D, Schigel D, Grimm V
Publié dans: Trends in Ecology & Evolution, Numéro 38, 2023, ISSN 0169-5347
Éditeur: Elsevier BV
DOI: 10.1016/J.TREE.2023.04.010

The role of seasonality in shaping the interactions of honeybees with other taxa

Auteurs: Helena Wirta, Mirkka Jones, Pablo Peña‐Aguilera, Camilo Chacón‐Duque, Eero Vesterinen, Otso Ovaskainen, Nerea Abrego, Tomas Roslin
Publié dans: Ecology and Evolution, Numéro 13, 2023, ISSN 2045-7758
Éditeur: Wiley
DOI: 10.1002/ECE3.10580

Prototype Biodiversity Digital Twin: Real-time bird monitoring with citizen-science data

Auteurs: Ovaskainen O, Lauha P, Lopez Gordillo J, Nokelainen O, Rahman AU, Souza AT, Talaskivi J, Tikhonov G, Vancraeyenest A, Lehtiö A
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/ARPHAPREPRINTS.E124640

Recording provenance of workflow runs with RO-Crate

Auteurs: Leo S, Crusoe M, Rodríguez-Navas L, Sirvent R, Kanitz A, De Geest P, Wittner R, Pireddu L, Garijo D, Fernández J, Colonnelli I, Gallo M, Ohta T, Suetake H, Capella-Gutierrez S, de Wit R, Kinoshita B, Soiland-Reyes S
Publié dans: PLOS One, Numéro 19(9), 2024, ISSN 1932-6203
Éditeur: PLOS
DOI: 10.48550/ARXIV.2312.07852

Prototype biodiversity digital twin: crop wild relatives genetic resources for food security

Auteurs: Chala D, Kusch E, Weiland C, Andrew C, Grieb J, Rossi T, Martinovic T, Endresen D
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e125192

Brood indicators are an early warning indicator of honey bee colony loss — a simulation-based study

Auteurs: Groeneveld J, Odemer R, Requier F
Publié dans: PLoS One, Numéro 19, 2024, ISSN 1932-6203
Éditeur: Public Library of Science (PLOS)
DOI: 10.1371/journal.pone.0302907

Prototype biodiversity digital twin: disease outbreaks

Auteurs: Ingenloff K, Ben Aziza S, Weiland C, Nikolova N, Thulke H-H, Lange M, Reichold A, Schigel D
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e125521

Prototype Biodiversity Digital Twin: grassland biodiversity dynamics

Auteurs: Taubert F, Rossi T, Wohner C, Venier S, Martinovič T, Khan T, Gordillo J, Banitz T
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/ARPHAPREPRINTS.E125077

Prototype Biodiversity Digital Twin: Phylogenetic Diversity

Auteurs: Mikryukov V, Abarenkov K, Jeppesen TS, Schigel D, Frøslev T
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e124988

WorkflowHub: a registry for computational workflows

Auteurs: Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José M. Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble
Publié dans: Scientific Data, Numéro 12, 2025, ISSN 2052-4463
Éditeur: Springer Nature Limited
DOI: 10.48550/ARXIV.2410.06941

Experimental evidence that root‐associated fungi improve plant growth at high altitude

Auteurs: Skylar Burg; Otso Ovaskainen; Brendan Furneaux; Natalia Ivanova; Arusyak Abrahamyan; Pekka Niittynen; Panu Somervuo; Nerea Abrego
Publié dans: Molecular Ecology, Numéro 33, 2024, ISSN 1365-294X
Éditeur: Wiley
DOI: 10.1111/MEC.17376

Prototype Biodiversity Digital Twin: Invasive Alien Species

Auteurs: Khan T, El-Gabbas A, Golivets M, Souza AT, Gordillo J, Kierans D, Kühn I
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e124579

Fragmented Networks: Challenges in communication and cohesion of European Biodiversity Research Infrastructures

Auteurs: Souza A, Martinovič T, Andrew C, Gan Y-M, Kusch E
Publié dans: Biodiversity Data Journal, Numéro 13, 2025, ISSN 1314-2828
Éditeur: Pensoft
DOI: 10.5281/ZENODO.13903241

Digital twin challenges in biodiversity modelling

Auteurs: Trantas A, Plug R, Pileggi P, Lazovik E
Publié dans: Ecological Informatics, Numéro 78, 2023, ISSN 1574-9541
Éditeur: Elsevier BV
DOI: 10.1016/j.ecoinf.2023.102357

Prototype Biodiversity Digital Twin: prioritisation of DNA metabarcoding sampling locations

Auteurs: Frøslev T, Boyd R, Schigel D
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft
DOI: 10.3897/rio.10.e124978

Developing Prototype Digital Twins for biodiversity conservation and management: achievements, challenges and perspectives

Auteurs: Damien Lecarpentier, Timea Biro, Dag Endresen, Marina Golivets, Volker Grimm, Sharif Islam, Hanna Koivula, Dirk Pleiter, Tuomas Rossi, Dmitry Schigel, Christoph Wohner, Gabriela Zuquim, Jesse Harrison
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, ISSN 2367-7163
Éditeur: Pensoft Publishers
DOI: 10.3897/RIO.10.E133474

Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting

Auteurs: Anis Ur Rahman, Gleb Tikhonov, Jari Oksanen, Tuomas Rossi, Otso Ovaskainen
Publié dans: PLOS Computational Biology, Numéro 20, 2024, ISSN 1553-7358
Éditeur: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PCBI.1011914

Conference proceedings (6)

Visualization Techniques and Tools for Developing Digital Twins of Ecosystems: State-of-the-Art and Selection

Auteurs: Ashraf, Adeela; Belleman, Robert; Zhao, Zhiming
Publié dans: 2023 IEEE Smart World Congress (SWC), 2024
Éditeur: IEEE
DOI: 10.1109/SWC57546.2023.10448753

Realising Distributed Digital Twins within Federated Digital Infrastructures

Auteurs: Kierans D & Pleiter D
Publié dans: Proceedings of the First International Workshop on Distributed Digital Twins (DiDit 2024) co-located with the 19th International Federated Conference on Distributed Computing Techniques (DisCoTec 2024), Numéro Vol 3755, 2024, ISSN 1613-0073
Éditeur: CEUR Workshop Proceedings, CEUR-WS.org

FDO as an Interoperability Framework for the Biodiversity Digital Twin Project

Auteurs: Lopez Gordillo J & Islam S 
Publié dans: Open Conference Proceedings, International FAIR Digital Objects Implementation Summit 2024, Numéro 5, 2025, ISSN 2749-5841
Éditeur: TIB Open Publishing
DOI: 10.52825/OCP.V5I.1190

Implementing FAIR Semantic Mappings Leveraging on RO-Crate

Auteurs: Grieb J, Weiland C, Wolodkin A, Lopez Gordillo J, Islam S
Publié dans: Open Conference Proceedings, International FAIR Digital Objects Implementation Summit 2024, Numéro 5, 2025, ISSN 2749-5841
Éditeur: TIB Open Publishing
DOI: 10.52825/OCP.V5I.1179

Uncertainty Quantification for Metamodels

Auteurs: Okánik M, Trantas A, de Bakker M.P, Lazovik E
Publié dans: Proceedings of the Thirteenth Symposium on Conformal and Probabilistic Prediction with Applications, Numéro 230, 2024, ISSN 2640-3498
Éditeur: ML Research Press

"Paper ""Digital Twin and Foundation Models: A New Frontier"" presented at the 16th International Conference on Agents and Artificial Intelligence (ICAART 2024)"

Auteurs: Trantas, A and Pileggi, P
Publié dans: Proceedings of the 16th International Conference on Agents and Artificial Intelligence , Numéro 3, 2024, ISSN 2184-433X
Éditeur: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0012427000003636