Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities

Información del proyecto

BioDT

Identificador del acuerdo de subvención: 101057437

DOI

10.3030/101057437

Proyecto cerrado

Fecha de la firma de la CE 31 Mayo 2022

Fecha de inicio 1 Junio 2022

Fecha de finalización 31 Mayo 2025

Financiado con arreglo a

• Research infrastructures

Coste total

€ 11 059 061,00

Aportación de la UE

€ 11 059 061,00

Coordinado por

CSC-TIETEEN TIETOTEKNIIKAN KESKUS OY
Finland

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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.

Publicaciones

Other (61)

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

Autores: Afsar B, Versluijs M, Eyvindson K, Ovaskainen O
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.15623398

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

Autores: Afsar B, Eyvindson K, Versluijs M, Ovaskainen O
Publicado en: IBFRA Conference 2023: Book of abstracts, Edición 77, 2023, ISSN 2342-7639
Editor: 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."

Autores: Groeneveld J, Wendt A, Grimm V
Publicado en: Book of Abstracts of 71. Jahrestagung der Arbeitsgemeinschaft der Institute für Bienenforschung e.V., 2024
Editor: Association of the German Bee Research Institutes

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

Autores: Weiland C, Grieb J, Bauer D, Chala D, Kusch E, Andrew C, Endresen D
Publicado en: Biodiversity Information Science and Standards, Edición 8, 2024, ISSN 2535-0897
Editor: 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

Autores: Ingenloff K
Publicado en: 2025
Editor: 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"

Autores: Nikolova N & Brewster C
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.15601987

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

Autores: Wolodkin A, Weiland C, Grieb J 
Publicado en: Biodiversity Information Science and Standards , Edición 7, 2023, ISSN 2535-0897
Editor: 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"

Autores: Soiland-Reyes S, Sefton P, Castro LJ, Coppens F, Garijo D, Leo S, Portier M, Groth P, Goble C
Publicado en: 1st International Conference on FAIR Digital Objects, Edición 1ST, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7245315

Guide for publishing biological survey data to GBIF

Autores: 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.
Publicado en: 2025
Editor: 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"

Autores: Khan T
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.15575560

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

Autores: Groeneveld J, Grimm V
Publicado en: Book of Abstracts of Strategiekonferenz der Deutschen Agrarforschungsallianz, 2024
Editor: Deutsche Agrarforschungsallianz (DAFA)

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

Autores: Soiland-Reyes S, Goble C
Publicado en: ELIXIR All Hands 2023, 2023
Editor: 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"

Autores: Islam S, Koivula H, Endresen D, Kusch E, Schigel D, Addink W 
Publicado en: Biodiversity Information Science and Standards, Edición 7, 2023, ISSN 2535-0897
Editor: Pensoft
DOI: 10.3897/BISS.7.112373

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

Autores: Souza A, Rasilo T, Bäck J 
Publicado en: Report Series Aerosol Science, Abstract Book of the ACCC-FASN Science Conference 2023, Edición 271, 2023, ISSN 2814-4236
Editor: The Finnish Association for Aerosol Research (FAAR)

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

Autores: Harrison J, Aalto T, Oostervink N, Geenen T
Publicado en: 2024
Editor: 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"

Autores: Souza A., Sara-aho K, Rolph S, Salamon O, Martinovič T
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.15269900

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

Autores: Dick J, Rolph S, Andrews C
Publicado en: Resilient Landscapes for People, Nature Climate. BES Symposium Book of Abstracts, 2024
Editor: British Ecological Society (BES)

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

Autores: Aalto T, Sara-aho K, Zuquim G, Pleiter D, Geenen T
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.13938825

BioDT poster at ISC High Performance 2023

Autores: Martinovic T, Drago F
Publicado en: ISC High Performance 2023, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8033683

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

Autores: 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
Publicado en: Reseach Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft

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

Autores: Khan T
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8313904

Metabarcoding Data Toolkit – user guide

Autores: Frøslev T
Publicado en: 2025
Editor: 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"

Autores: Islam S
Publicado en: Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8144429

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

Autores: Koivula H, Wohner C, Magagna B, d`Aragona P, Oggioni A 
Publicado en: Biodiversity Information Science and Standards , Edición 7, 2023, ISSN 2535-0897
Editor: 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"

Autores: Chala, D
Publicado en: Living Norway Colloquium 2023, 2023
Editor: 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)"

Autores: Trantas A, Pileggi, P
Publicado en: ICAART 2024 Final Program and Book of Abstracts, 2024
Editor: SCITEPRESS - Science and Technology Publications

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

Autores: Soiland-Reyes S, Castro LJ, Garijo D, Portier M, Goble C, Groth P
Publicado en: 1st International Conference on FAIR Digital Objects, Edición 1ST, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7256428

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

Autores: Taubert F, De Bakke M, Banitz T, Grimm V, Groeneveld J, Ovaskainen O
Publicado en: ECEM 2023 Book of Abstracts, 2023
Editor: 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"

Autores: Islam S
Publicado en: FAIR Digital Objects Forum lecture Concept of Digital Twins /Surrogate, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7852889

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

Autores: Andrew C, Islam S, Weiland C, Endresen D
Publicado en: 2024, ISSN 2331-8422
Editor: ArXiv / Cornell University
DOI: 10.48550/ARXIV.2405.19857

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

Autores: Souza A, Rasilo T, Bäck J
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.10203382

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

Autores: Bauer, D., Kusch, E., Weiland, C., Grieb, J., Chala, D., & Endresen, D. 
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.13928655

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

Autores: Rossi T & Martinovič T 
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.15536282

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

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

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

Autores: Groeneveld J, Krebs J, Martinovic T, Rossi T, Wendt A, Grimm V
Publicado en: NHR Conference '23 Book of Abstracts, 2023
Editor: 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"

Autores: Groeneveld, J.
Publicado en: 2025
Editor: 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"

Autores: Dick J, Rolph S, Andrews C, Watkins J
Publicado en: workshop at Cairngorms National Park, 2023
Editor: 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 "

Autores: Islam S
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.13982672

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

Autores: Zuquim G
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.12166859

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

Autores: Soiland-Reyes S, Castro LJ
Publicado en: Overview of FAIR data publishing with bioschemas & RO-Crate, 2023
Editor: F1000 Research
DOI: 10.7490/f1000research.1119459.1

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

Autores: Rahman A, Tikhonov G, Oksanen J, Rossi T, Ovaskainen O
Publicado en: 2024, ISSN 2692-8205
Editor: 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"

Autores: Dick J, Andrews C, Rolph S, Watkins J
Publicado en: A digital twin linking recreational potential and biodiversity in the Cairngorms National Park, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8038203

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

Autores: Broekhuijsen, J
Publicado en: Digitalisation for Sustainable Nature, 2022
Editor: 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)"

Autores: Groeneveld J, Krebs J, Martinovic T, Rossi T, Wendt A, Grimm V
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.12580924

BioDT poster at EuroHPC Summit 2023

Autores: Drago, Federico; Pleiter, Dirk; Martinovic, Tomas
Publicado en: EuroHPC 2023, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7754745

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

Autores: Taubert F, Banitz T, Rossi T, Wohner C, Venier S, Martinovič T, Khan T, Lopez Gordillo, J
Publicado en: 2025
Editor: Zenodo

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

Autores: Wohner C, Oggioni A, Tagliolato P, Taubert F, Banitz T, Venier S, Trembath P and Peterseil J
Publicado en: 2024
Editor: 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"

Autores: Soiland-Reyes S, Leo S, Castro LJ, Sefton P, Goble C
Publicado en: ELIXIR, 2023
Editor: 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"

Autores: Islam S, Lopez Gordillo J, Endresen D, Andrew C 
Publicado en: Biodiversity Information Science and Standards, Edición 8, 2024, ISSN 2535-0897
Editor: 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?"

Autores: Le Franc Y,  Harmse H, De Santis L, Jeffery K, Matentzoglu N, Weiland C
Publicado en: 2023
Editor: 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"

Autores: Ingenloff K
Publicado en: ARPHA Conference Abstracts, Edición 8, 2025, ISSN 2603-3925
Editor: Pensoft
DOI: 10.3897/ACA.8.E151692

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

Autores: Goble C, Soiland-Reyes S
Publicado en: Sharing research artefacts as FAIR Digital Objects using RO-Crate, 2023
Editor: 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"

Autores: Soiland-Reyes S, Goble C
Publicado en: Building diverse FDO Collections using RO-Crate: An overview of the RO-Crate concept and its implementations, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7915603

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

Autores: Schigel D
Publicado en: Biodiversity Information Science and Standards, Edición 8, 2024, ISSN 2535-0897
Editor: Pensoft
DOI: 10.3897/BISS.8.139100

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

Autores: 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.
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.14331464

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

Autores: 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
Publicado en: Biodiversity Information Science and Standards , Edición 7, 2023, ISSN 2535-0897
Editor: Pensoft
DOI: 10.3897/biss.7.111427

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

Autores: Groeneveld J, Wendt A, Krebs J, Grimm V
Publicado en: ECEM 2023 Book of Abstracts, 2023
Editor: 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"

Autores: Chala, D
Publicado en: 2023
Editor: 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"

Autores: Islam S, Weiland C, Addink W
Publicado en: Research Ideas and Outcomes, Edición 8, 2022, ISSN 2367-7163
Editor: Pensoft Publishers
DOI: 10.3897/RIO.8.E93816

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

Autores: Islam S
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.15553776

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

Autores: Martinovič T, Sara-aho K, Salamon O, Rolph S, Souza A
Publicado en: Biodiversity Information Science and Standards, Edición 8, 2024, ISSN 2535-0897
Editor: Pensoft
DOI: 10.3897/BISS.8.135092

Peer reviewed articles (25)

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Autores: Soiland-Reyes S, Goble C, Groth P.
Publicado en: PeerJ Comput Sci, 2024, ISSN 2376-5992
Editor: San Diego CA: PeerJ Inc
DOI: 10.48550/arXiv.2306.07436

Prototype biodiversity digital twin: Forest biodiversity dynamics

Autores: Afsar B, Eyvindson K, Rossi T, Versluijs M, Ovaskainen O
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e125086

rdata: A Python library for R datasets

Autores: Carlos Ramos-Carreño, Tuomas Rossi
Publicado en: Journal of Open Source Software, Edición 9, 2024, ISSN 2475-9066
Editor: Journal of Open Source Software
DOI: 10.21105/JOSS.07540

High-resolution spatiotemporal forecasting of the European crane migration

Autores: De Koning K, Nilsson L, Månsson J, Ovaskainen O, Kranstauber B, Arp M, Schakel JK
Publicado en: Ecological Modelling, Edición 498, 2024, ISSN 0304-3800
Editor: Elsevier BV
DOI: 10.1016/j.ecolmodel.2024.110884

Prototype biodiversity digital twin: honey bees in agricultural landscapes

Autores: Groeneveld V, Martinovic T, Rossi T, Salamon O, Sara-aho K, Grimm V
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e125167

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

Autores: Luttermann M, Prestele R, Grimm V, Groeneveld J
Publicado en: Ecology and Evolution, Edición 15, 2025, ISSN 2045-7758
Editor: John Wiley and Sons
DOI: 10.1002/ECE3.71468

Prototype Digital Twin: Recreation and biodiversity cultural ecosystem services

Autores: 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
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/ARPHAPREPRINTS.E125515

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

Autores: 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
Publicado en: Citizen Science: Theory and Practice, Edición 9, 2024, ISSN 2057-4991
Editor: Ubiquity Press, Ltd.
DOI: 10.5334/CSTP.710

Digital twins: dynamic model-data fusion for ecology

Autores: de Koning K, Broekhuijsen J, Kühn I, Ovaskainen O, Taubert F, Endresen D, Schigel D, Grimm V
Publicado en: Trends in Ecology & Evolution, Edición 38, 2023, ISSN 0169-5347
Editor: Elsevier BV
DOI: 10.1016/J.TREE.2023.04.010

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

Autores: Helena Wirta, Mirkka Jones, Pablo Peña‐Aguilera, Camilo Chacón‐Duque, Eero Vesterinen, Otso Ovaskainen, Nerea Abrego, Tomas Roslin
Publicado en: Ecology and Evolution, Edición 13, 2023, ISSN 2045-7758
Editor: Wiley
DOI: 10.1002/ECE3.10580

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

Autores: Ovaskainen O, Lauha P, Lopez Gordillo J, Nokelainen O, Rahman AU, Souza AT, Talaskivi J, Tikhonov G, Vancraeyenest A, Lehtiö A
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/ARPHAPREPRINTS.E124640

Recording provenance of workflow runs with RO-Crate

Autores: 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
Publicado en: PLOS One, Edición 19(9), 2024, ISSN 1932-6203
Editor: PLOS
DOI: 10.48550/ARXIV.2312.07852

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

Autores: Chala D, Kusch E, Weiland C, Andrew C, Grieb J, Rossi T, Martinovic T, Endresen D
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e125192

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

Autores: Groeneveld J, Odemer R, Requier F
Publicado en: PLoS One, Edición 19, 2024, ISSN 1932-6203
Editor: Public Library of Science (PLOS)
DOI: 10.1371/journal.pone.0302907

Prototype biodiversity digital twin: disease outbreaks

Autores: Ingenloff K, Ben Aziza S, Weiland C, Nikolova N, Thulke H-H, Lange M, Reichold A, Schigel D
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e125521

Prototype Biodiversity Digital Twin: grassland biodiversity dynamics

Autores: Taubert F, Rossi T, Wohner C, Venier S, Martinovič T, Khan T, Gordillo J, Banitz T
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/ARPHAPREPRINTS.E125077

Prototype Biodiversity Digital Twin: Phylogenetic Diversity

Autores: Mikryukov V, Abarenkov K, Jeppesen TS, Schigel D, Frøslev T
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e124988

WorkflowHub: a registry for computational workflows

Autores: 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
Publicado en: Scientific Data, Edición 12, 2025, ISSN 2052-4463
Editor: Springer Nature Limited
DOI: 10.48550/ARXIV.2410.06941

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

Autores: Skylar Burg; Otso Ovaskainen; Brendan Furneaux; Natalia Ivanova; Arusyak Abrahamyan; Pekka Niittynen; Panu Somervuo; Nerea Abrego
Publicado en: Molecular Ecology, Edición 33, 2024, ISSN 1365-294X
Editor: Wiley
DOI: 10.1111/MEC.17376

Prototype Biodiversity Digital Twin: Invasive Alien Species

Autores: Khan T, El-Gabbas A, Golivets M, Souza AT, Gordillo J, Kierans D, Kühn I
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e124579

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

Autores: Souza A, Martinovič T, Andrew C, Gan Y-M, Kusch E
Publicado en: Biodiversity Data Journal, Edición 13, 2025, ISSN 1314-2828
Editor: Pensoft
DOI: 10.5281/ZENODO.13903241

Digital twin challenges in biodiversity modelling

Autores: Trantas A, Plug R, Pileggi P, Lazovik E
Publicado en: Ecological Informatics, Edición 78, 2023, ISSN 1574-9541
Editor: Elsevier BV
DOI: 10.1016/j.ecoinf.2023.102357

Prototype Biodiversity Digital Twin: prioritisation of DNA metabarcoding sampling locations

Autores: Frøslev T, Boyd R, Schigel D
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft
DOI: 10.3897/rio.10.e124978

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

Autores: 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
Publicado en: Research Ideas and Outcomes, Edición 10, 2024, ISSN 2367-7163
Editor: Pensoft Publishers
DOI: 10.3897/RIO.10.E133474

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

Autores: Anis Ur Rahman, Gleb Tikhonov, Jari Oksanen, Tuomas Rossi, Otso Ovaskainen
Publicado en: PLOS Computational Biology, Edición 20, 2024, ISSN 1553-7358
Editor: 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

Autores: Ashraf, Adeela; Belleman, Robert; Zhao, Zhiming
Publicado en: 2023 IEEE Smart World Congress (SWC), 2024
Editor: IEEE
DOI: 10.1109/SWC57546.2023.10448753

Realising Distributed Digital Twins within Federated Digital Infrastructures

Autores: Kierans D & Pleiter D
Publicado en: 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), Edición Vol 3755, 2024, ISSN 1613-0073
Editor: CEUR Workshop Proceedings, CEUR-WS.org

FDO as an Interoperability Framework for the Biodiversity Digital Twin Project

Autores: Lopez Gordillo J & Islam S 
Publicado en: Open Conference Proceedings, International FAIR Digital Objects Implementation Summit 2024, Edición 5, 2025, ISSN 2749-5841
Editor: TIB Open Publishing
DOI: 10.52825/OCP.V5I.1190

Implementing FAIR Semantic Mappings Leveraging on RO-Crate

Autores: Grieb J, Weiland C, Wolodkin A, Lopez Gordillo J, Islam S
Publicado en: Open Conference Proceedings, International FAIR Digital Objects Implementation Summit 2024, Edición 5, 2025, ISSN 2749-5841
Editor: TIB Open Publishing
DOI: 10.52825/OCP.V5I.1179

Uncertainty Quantification for Metamodels

Autores: Okánik M, Trantas A, de Bakker M.P, Lazovik E
Publicado en: Proceedings of the Thirteenth Symposium on Conformal and Probabilistic Prediction with Applications, Edición 230, 2024, ISSN 2640-3498
Editor: 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)"

Autores: Trantas, A and Pileggi, P
Publicado en: Proceedings of the 16th International Conference on Agents and Artificial Intelligence , Edición 3, 2024, ISSN 2184-433X
Editor: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0012427000003636