Periodic Reporting for period 3 - BioDT (Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities)
Reporting period: 2024-06-01 to 2025-05-31
Biodiversity is crucial for food security, medicinal sources, socioeconomic benefits, cultural and aesthetic values, and ecosystem resilience under global change. Biodiversity science combines fields including ecology, biology, genetics, economics, and geography, which often have a relatively short history of computational research. However, research in the field is becoming increasingly data-intensive and models more complex, requiring the use of supercomputers. This is connected to a need for improved modelling approaches that can handle large volumes of data and produce reliable predictions of biodiversity shifts in response to pressures including changes in climate and land-use. Biodiversity data are also diverse in terms of their quality, coverage, and openness. Successfully considering biodiversity as part of decision-making therefore requires access to increasingly harmonised, open, and quality-controlled data.
The Digital Twins (DTs) concept represents a solution to address the needs of modern biodiversity research. A digital twin can be defined as a virtual, interactive replica of a real-world entity or process, consisting of data, a model (the digital representation of a real-world process), and methods to connect the data and the model.
The Horizon Europe Biodiversity Digital Twin (BioDT) project advanced the frontiers of biodiversity science by developing prototypes of DTs of different aspects of biodiversity dynamics. The DTs developed are deployed by leveraging EuroHPC world-class supercomputers such as LUMI and Karolina and national computational resources. BioDT addressed the following key objectives:
1- Building and deploying prototype DTs corresponding to several biodiversity topics
2- Integrating the DTs with research infrastructures that play a key role in facilitating access to biodiversity data
3- Ensuring the interoperability of BioDT with the EC flagship programme Destination Earth
Through its work on demonstrating the technological feasibility of DTs in ecological research and facilitating access to biodiversity data, BioDT paved the way for groundbreaking changes in ecology, including establishing new types of interactive tools for monitoring ecosystem health, with benefits for a broad range of end-users, including citizens, researchers, and policymakers.
The Digital Twins (DTs) concept represents a solution to address the needs of modern biodiversity research. A digital twin can be defined as a virtual, interactive replica of a real-world entity or process, consisting of data, a model (the digital representation of a real-world process), and methods to connect the data and the model.
The Horizon Europe Biodiversity Digital Twin (BioDT) project advanced the frontiers of biodiversity science by developing prototypes of DTs of different aspects of biodiversity dynamics. The DTs developed are deployed by leveraging EuroHPC world-class supercomputers such as LUMI and Karolina and national computational resources. BioDT addressed the following key objectives:
1- Building and deploying prototype DTs corresponding to several biodiversity topics
2- Integrating the DTs with research infrastructures that play a key role in facilitating access to biodiversity data
3- Ensuring the interoperability of BioDT with the EC flagship programme Destination Earth
Through its work on demonstrating the technological feasibility of DTs in ecological research and facilitating access to biodiversity data, BioDT paved the way for groundbreaking changes in ecology, including establishing new types of interactive tools for monitoring ecosystem health, with benefits for a broad range of end-users, including citizens, researchers, and policymakers.
BioDT has deployed nine prototypes of Digital Twins (pDTs) that are grouped around four main biodiversity topics:
- Species responses to environmental change
- Dynamics and threats from and for species of policy concern
- Species interaction with each other and with humans
- Genetically detected biodiversity
The pDTs are composed of several components and include features for moving data that serve as input into modelling tools and the project has established methods for collecting data to feed the pDTs via citizen science campaigns. Each pDT relies, as far as possible, on open-access components and data from research infrastructures.
Moreover, BioDT developed a platform for the creation of new prototypes and for further enhancing existing pDTs. The BioDT Platform allows access to federated data, HPC resources, and graphical user interface development. It is intended as an easy-to-access environment where end-users can interact with DTs, including running them on the LUMI supercomputer. By combining different modelling methods in new ways and enabling easier model-user interaction, BioDT has developed unprecedented understanding of biodiversity shifts across time and space, providing foundational blueprints for advancing Biodiversity Digital Twins. These innovations enable more effective responses to biodiversity challenges posed by climate change and land-use impacts.
- Species responses to environmental change
- Dynamics and threats from and for species of policy concern
- Species interaction with each other and with humans
- Genetically detected biodiversity
The pDTs are composed of several components and include features for moving data that serve as input into modelling tools and the project has established methods for collecting data to feed the pDTs via citizen science campaigns. Each pDT relies, as far as possible, on open-access components and data from research infrastructures.
Moreover, BioDT developed a platform for the creation of new prototypes and for further enhancing existing pDTs. The BioDT Platform allows access to federated data, HPC resources, and graphical user interface development. It is intended as an easy-to-access environment where end-users can interact with DTs, including running them on the LUMI supercomputer. By combining different modelling methods in new ways and enabling easier model-user interaction, BioDT has developed unprecedented understanding of biodiversity shifts across time and space, providing foundational blueprints for advancing Biodiversity Digital Twins. These innovations enable more effective responses to biodiversity challenges posed by climate change and land-use impacts.
BioDT was a pioneering project in adapting the concept of Digital Twins to tackle biodiversity challenges. BioDT advanced in the readiness of biodiversity data and modelling tools to HPC environments, allowing timely and efficient access to reliable and up-to-date results, in some cases even near real-time. The nine launched prototypes have a graphical user interface that can be accessed via web browsers, allowing users to:
1- Understand the growth dynamics and improve the management of temperate grassland for sites across Europe (Grassland pDT)
2- Simulate expected honey production and bee population dynamics in targeted locations and applying different parasite prevention strategies (HoneyBee pDT)
3- Investigate the impact of different forest management strategies and climate change scenarios on forests and biodiversity (Forest pDT)
4- Visualize bird species observations and patterns across Finland to explore bird migration, population trends, and species diversity (Real-Time Bird Monitoring pDT)
5- Personalize maps of the recreation potential and biodiversity distribution of a national park according to user expectations (Cultural Ecosystem Services pDT)
6- Identify and map populations of crop wild relatives adapted to extreme conditions such as high or low temperatures, soil acidity, salinity, or drought, to tap into valuable traits for widening the genetic bases of crops (Crop Wild Relatives pDT)
7- Simulate infection dynamics in the wild boar population in support of management decisions in response to the spread of African swine fever in European wild boar populations (Disease Outbreaks pDT)
8- Visualize projections of the distribution of invasive alien plant species in Europe and the predicted level of invasion under current and future climate scenarios (Invasive Species pDT)
9- Calculate and visualize phylogenetic biodiversity distribution from local to global scales. Phylogenetic biodiversity metrics can be complementary or even more informative than traditional biodiversity indexes such as species richness because they capture evolutionary relationships between species (PhyloNext pDT)
The BioDT project has identified several key needs in advancing FAIR principles (Findability, Accessibility, Interoperability, and Reusability) in relation to biodiversity data and has made significant technical progress in the development of tools for the deployment of new DTs. The pDTs serve as a blueprint for further development were also used for educational purposes. Through pioneering work on FAIR-compliant DTs, the project facilitated further work in this field by connecting DTs with data supplied through European biodiversity research infrastructures.
BioDT demonstrated multiple feasible ways in which the digital twins’ approach can be applied to the biodiversity domain. The feedback gathered from end-users is contributing toward the successful uptake of pDTs by ensuring their alignment with stakeholders’ needs and increasing user literacy. Finally, integration with major EU initiatives has been strengthened. Ongoing discussions are focused on demonstrating how specific pDTs can be connected to initiatives such as the Destination Earth, support the European Open Science Cloud and promote open science and science-based policy-making across Europe.
1- Understand the growth dynamics and improve the management of temperate grassland for sites across Europe (Grassland pDT)
2- Simulate expected honey production and bee population dynamics in targeted locations and applying different parasite prevention strategies (HoneyBee pDT)
3- Investigate the impact of different forest management strategies and climate change scenarios on forests and biodiversity (Forest pDT)
4- Visualize bird species observations and patterns across Finland to explore bird migration, population trends, and species diversity (Real-Time Bird Monitoring pDT)
5- Personalize maps of the recreation potential and biodiversity distribution of a national park according to user expectations (Cultural Ecosystem Services pDT)
6- Identify and map populations of crop wild relatives adapted to extreme conditions such as high or low temperatures, soil acidity, salinity, or drought, to tap into valuable traits for widening the genetic bases of crops (Crop Wild Relatives pDT)
7- Simulate infection dynamics in the wild boar population in support of management decisions in response to the spread of African swine fever in European wild boar populations (Disease Outbreaks pDT)
8- Visualize projections of the distribution of invasive alien plant species in Europe and the predicted level of invasion under current and future climate scenarios (Invasive Species pDT)
9- Calculate and visualize phylogenetic biodiversity distribution from local to global scales. Phylogenetic biodiversity metrics can be complementary or even more informative than traditional biodiversity indexes such as species richness because they capture evolutionary relationships between species (PhyloNext pDT)
The BioDT project has identified several key needs in advancing FAIR principles (Findability, Accessibility, Interoperability, and Reusability) in relation to biodiversity data and has made significant technical progress in the development of tools for the deployment of new DTs. The pDTs serve as a blueprint for further development were also used for educational purposes. Through pioneering work on FAIR-compliant DTs, the project facilitated further work in this field by connecting DTs with data supplied through European biodiversity research infrastructures.
BioDT demonstrated multiple feasible ways in which the digital twins’ approach can be applied to the biodiversity domain. The feedback gathered from end-users is contributing toward the successful uptake of pDTs by ensuring their alignment with stakeholders’ needs and increasing user literacy. Finally, integration with major EU initiatives has been strengthened. Ongoing discussions are focused on demonstrating how specific pDTs can be connected to initiatives such as the Destination Earth, support the European Open Science Cloud and promote open science and science-based policy-making across Europe.