Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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.

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.

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.

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

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

Author(s): Afsar B, Eyvindson K, Versluijs M, Ovaskainen O
Published in: IBFRA Conference 2023: Book of abstracts, Issue 77, 2023, ISSN 2342-7639
Publisher: 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."

Author(s): Groeneveld J, Wendt A, Grimm V
Published in: Book of Abstracts of 71. Jahrestagung der Arbeitsgemeinschaft der Institute für Bienenforschung e.V., 2024
Publisher: Association of the German Bee Research Institutes

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

Author(s): Wolodkin A, Weiland C, Grieb J
Published in: Biodiversity Information Science and Standards , Issue 7, 2023, ISSN 2535-0897
Publisher: 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"

Author(s): Soiland-Reyes S, Sefton P, Castro LJ, Coppens F, Garijo D, Leo S, Portier M, Groth P, Goble C
Published in: 1st International Conference on FAIR Digital Objects, Issue 1ST, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7245315

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

Author(s): Groeneveld J, Grimm V
Published in: Book of Abstracts of Strategiekonferenz der Deutschen Agrarforschungsallianz, 2024
Publisher: Deutsche Agrarforschungsallianz (DAFA)

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

Author(s): Soiland-Reyes S, Goble C
Published in: ELIXIR All Hands 2023, 2023
Publisher: 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"

Author(s): Islam S, Koivula H, Endresen D, Kusch E, Schigel D, Addink W
Published in: Biodiversity Information Science and Standards, Issue 7, 2023, ISSN 2535-0897
Publisher: Pensoft
DOI: 10.3897/biss.7.112373

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

Author(s): Souza A, Rasilo T, Bäck J
Published in: Report Series Aerosol Science, Abstract Book of the ACCC-FASN Science Conference 2023, Issue 271, 2023, ISSN 2814-4236
Publisher: The Finnish Association for Aerosol Research (FAAR)

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

Author(s): Harrison J, Aalto T, Oostervink N, Geenen T
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.12722280

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

Author(s): Dick J, Rolph S, Andrews C
Published in: Resilient Landscapes for People, Nature Climate. BES Symposium Book of Abstracts, 2024
Publisher: British Ecological Society (BES)

BioDT poster at ISC High Performance 2023

Author(s): Martinovic T, Drago F
Published in: ISC High Performance 2023, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8033683

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

Author(s): Khan T
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8313904

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

Author(s): Islam S
Published in: Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8144429

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

Author(s): Koivula H, Wohner C, Magagna B, d`Aragona P, Oggioni A
Published in: Biodiversity Information Science and Standards , Issue 7, 2023, ISSN 2535-0897
Publisher: Pensoft
DOI: 10.3897/biss.7.112221

"Preprint ""Recording provenance of workflow runs with RO-Crate"""

Author(s): 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
Published in: 2023, ISSN 2331-8422
Publisher: ArXiv / Cornell University
DOI: 10.48550/arXiv.2312.07852

"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"

Author(s): Chala, D
Published in: Living Norway Colloquium 2023, 2023
Publisher: 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)"

Author(s): Trantas A, Pileggi, P
Published in: ICAART 2024 Final Program and Book of Abstracts, 2024
Publisher: SCITEPRESS - Science and Technology Publications

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

Author(s): Soiland-Reyes S, Castro LJ, Garijo D, Portier M, Goble C, Groth P
Published in: 1st International Conference on FAIR Digital Objects, Issue 1ST, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7256428

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

Author(s): Taubert F, De Bakke M, Banitz T, Grimm V, Groeneveld J, Ovaskainen O
Published in: ECEM 2023 Book of Abstracts, 2023
Publisher: Helmholtz Centre for Environmental Research GmbH (UFZ)

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

Author(s): Islam S
Published in: FAIR Digital Objects Forum lecture Concept of Digital Twins /Surrogate, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7852889

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

Author(s): Andrew C, Islam S, Weiland C, Endresen D
Published in: 2024, ISSN 2331-8422
Publisher: ArXiv / Cornell University
DOI: 10.48550/arXiv.2405.19857

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

Author(s): Souza A, Rasilo T, Bäck J
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.10203382

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

Author(s): Leo S, Rodríguez-Navas L, Fernández JM, De Geest P, Pireddu L, Crusoe MR, Garijo D, Colonnelli I, Sirvent R, Soiland-Reyes S
Published in: ELIXIR All Hands 2023, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8004793

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

Author(s): Groeneveld J, Krebs J, Martinovic T, Rossi T, Wendt A, Grimm V
Published in: NHR Conference '23 Book of Abstracts, 2023
Publisher: National High Performance Computing (NHR Alliance)

"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"

Author(s): Dick J, Rolph S, Andrews C, Watkins J
Published in: workshop at Cairngorms National Park, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8038537

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

Author(s): Soiland-Reyes S, Castro LJ
Published in: Overview of FAIR data publishing with bioschemas & RO-Crate, 2023
Publisher: F1000 Research
DOI: 10.7490/f1000research.1119459.1

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

Author(s): Rahman A, Tikhonov G, Oksanen J, Rossi T, Ovaskainen O
Published in: 2024, ISSN 2692-8205
Publisher: 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"

Author(s): Dick J, Andrews C, Rolph S, Watkins J
Published in: A digital twin linking recreational potential and biodiversity in the Cairngorms National Park, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8038203

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

Author(s): Broekhuijsen, J
Published in: Digitalisation for Sustainable Nature, 2022
Publisher: 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)"

Author(s): Groeneveld J, Krebs J, Martinovic T, Rossi T, Wendt A, Grimm V
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.12580924

BioDT poster at EuroHPC Summit 2023

Author(s): Drago, Federico; Pleiter, Dirk; Martinovic, Tomas
Published in: EuroHPC 2023, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7754745

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

Author(s): Wohner C, Oggioni A, Tagliolato P, Taubert F, Banitz T, Venier S, Trembath P and Peterseil J
Published in: 2024
Publisher: 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"

Author(s): Soiland-Reyes S, Leo S, Castro LJ, Sefton P, Goble C
Published in: ELIXIR, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8004796

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

Author(s): Le Franc Y, Harmse H, De Santis L, Jeffery K, Matentzoglu N, Weiland C
Published in: Show and Tell: BioDT and DISSCo Perspective, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8162873

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

Author(s): Goble C, Soiland-Reyes S
Published in: Sharing research artefacts as FAIR Digital Objects using RO-Crate, 2023
Publisher: 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"

Author(s): Soiland-Reyes S, Goble C
Published in: Building diverse FDO Collections using RO-Crate: An overview of the RO-Crate concept and its implementations, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7915603

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

Author(s): 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
Published in: Biodiversity Information Science and Standards , Issue 7, 2023, ISSN 2535-0897
Publisher: Pensoft
DOI: 10.3897/biss.7.111427

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

Author(s): Groeneveld J, Wendt A, Krebs J, Grimm V
Published in: ECEM 2023 Book of Abstracts, 2023
Publisher: 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"

Author(s): Chala, D
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.10055794

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Author(s): Soiland-Reyes S, Goble C, Groth P.
Published in: PeerJ Comput Sci, 2024, ISSN 2376-5992
Publisher: San Diego CA: PeerJ Inc
DOI: 10.48550/arXiv.2306.07436

Prototype biodiversity digital twin: Forest biodiversity dynamics

Author(s): Afsar B, Eyvindson K, Rossi T, Versluijs M, Ovaskainen O
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e125086

Prototype biodiversity digital twin: honey bees in agricultural landscapes

Author(s): Groeneveld V, Martinovic T, Rossi T, Salamon O, Sara-aho K, Grimm V
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e125167

Prototype Digital Twin: Recreation and biodiversity cultural ecosystem services

Author(s): 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
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e125450

Trends in Ecology and Ecolution

Author(s): de Koning K, Broekhuijsen J, Kühn I, Ovaskainen O, Taubert F, Endresen D, Schigel D, Grimm V
Published in: Trends in Ecology & Evolution, Issue 38, 2023, ISSN 0169-5347
Publisher: Elsevier BV
DOI: 10.1016/j.tree.2023.04.010

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

Author(s): Ovaskainen O, Lauha P, Lopez Gordillo J, Nokelainen O, Rahman AU, Souza AT, Talaskivi J, Tikhonov G, Vancraeyenest A, Lehtiö A
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e125523

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

Author(s): Chala D, Kusch E, Weiland C, Andrew C, Grieb J, Rossi T, Martinovic T, Endresen D
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e125192

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

Author(s): Groeneveld J, Odemer R, Requier F
Published in: PLoS One, Issue 19, 2024, ISSN 1932-6203
Publisher: Public Library of Science (PLOS)
DOI: 10.1371/journal.pone.0302907

Prototype biodiversity digital twin: disease outbreaks

Author(s): Ingenloff K, Ben Aziza S, Weiland C, Nikolova N, Thulke H-H, Lange M, Reichold A, Schigel D
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e125521

Prototype Biodiversity Digital Twin: grassland biodiversity dynamics

Author(s): Taubert F, Rossi T, Wohner C, Venier S, Martinovič T, Khan T, Gordillo J, Banitz T
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e124168

Prototype Biodiversity Digital Twin: Phylogenetic Diversity

Author(s): Mikryukov V, Abarenkov K, Jeppesen TS, Schigel D, Frøslev T
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e124988

Prototype Biodiversity Digital Twin: Invasive Alien Species

Author(s): Khan T, El-Gabbas A, Golivets M, Souza AT, Gordillo J, Kierans D, Kühn I
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e124579

Digital twin challenges in biodiversity modelling

Author(s): Trantas A, Plug R, Pileggi P, Lazovik E
Published in: Ecological Informatics, Issue 78, 2023, ISSN 1574-9541
Publisher: Elsevier BV
DOI: 10.1016/j.ecoinf.2023.102357

Prototype Biodiversity Digital Twin: prioritisation of DNA metabarcoding sampling locations

Author(s): Frøslev T, Boyd R, Schigel D
Published in: Research Ideas and Outcomes, Issue 10, 2024, ISSN 2367-7163
Publisher: Pensoft
DOI: 10.3897/rio.10.e124978

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

Author(s): Trantas, A and Pileggi, P
Published in: Proceedings of the 16th International Conference on Agents and Artificial Intelligence , Issue 3, 2024, ISSN 2184-433X
Publisher: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0012427000003636

"Conference 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"

Author(s): Islam S, Weiland C, Addink W
Published in: Research Ideas and Outcomes, Issue 8, 2022, ISSN 2367-7163
Publisher: Pensoft Publishers
DOI: 10.3897/rio.8.e93816

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