Periodic Reporting for period 2 - BioDT (Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities)
Periodo di rendicontazione: 2023-06-01 al 2024-05-31
Biodiversity is crucial for food security, medicinal source, socioeconomic benefits, cultural and aesthetic value, and ecosystem resilience under global change, enables species evolution and adaptation, and carries ethical significance from the standpoint of preserving life. Biodiversity data, such as data on species distributions, are used to monitor ecosystem health, guide conservation efforts and inform policy-making. Biodiversity is recognised in several European policy initiatives and flagship programmes, including the EU Biodiversity Strategy 2030, the EU Green Deal, UN Sustainable Development Goals, the Kunming-Montreal Global Biodiversity Framework and Destination Earth.
Biodiversity science combines fields including ecology, biology, genetics, economics and geography, which often have a relatively short history of computational research. While traditionally the processing of biodiversity data has not required substantial computing resources, research in the field is becoming increasingly data-intensive, requiring the use of supercomputers. This is connected to a need for improved modelling approaches that can handle large data masses 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.
Digital twins (DT) represent a highly promising 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, comprised of data, a model (the digital representation of a real-world process), and ways to connect the data and model.
The Horizon Europe Biodiversity Digital Twin (BioDT) project seeks to push the limits of biodiversity science by developing DT prototypes that mimic and predict different aspects of biodiversity dynamics, with the goal of improving our understanding of how biodiversity responds to diverse environmental pressures. As detailed and realistic simulations require large amounts of computing resources, the DTs developed in the project are deployed on the EuroHPC LUMI supercomputer, the top-ranking high-performance computing facility in Europe.
BioDT addresses 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 is anticipated to pave the way for system 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, policymakers and industry.
Biodiversity science combines fields including ecology, biology, genetics, economics and geography, which often have a relatively short history of computational research. While traditionally the processing of biodiversity data has not required substantial computing resources, research in the field is becoming increasingly data-intensive, requiring the use of supercomputers. This is connected to a need for improved modelling approaches that can handle large data masses 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.
Digital twins (DT) represent a highly promising 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, comprised of data, a model (the digital representation of a real-world process), and ways to connect the data and model.
The Horizon Europe Biodiversity Digital Twin (BioDT) project seeks to push the limits of biodiversity science by developing DT prototypes that mimic and predict different aspects of biodiversity dynamics, with the goal of improving our understanding of how biodiversity responds to diverse environmental pressures. As detailed and realistic simulations require large amounts of computing resources, the DTs developed in the project are deployed on the EuroHPC LUMI supercomputer, the top-ranking high-performance computing facility in Europe.
BioDT addresses 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 is anticipated to pave the way for system 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, policymakers and industry.
During its first two years of operation, the BioDT project identified key requirements for building and running biodiversity DTs and started the development of a technical platform for their use. The platform is intended as an easy-to-access environment where end-users can interact with DTs, including running them on the LUMI supercomputer.
BioDT has established 10 prototype DTs (pDTs) that are being developed as the project progresses. The prototypes are grouped around four main topics which are Species responses to environmental change; Dynamics and threats from and for species of policy concern; Species interaction with each other and with humans and Genetically detected Biodiversity. The pDTs cover a broad spectrum of Biodiversity subtopics, from grassland productivity and diversity according to environmental conditions and management strategies; to population dynamics and honey production of bees; to the cultural value of biodiversity and to identifying locations of potential climate-resilient wild crop relatives occurrances.
The digital twins designed in BioDT are made of several components and include, for example, features for moving data and feeding them to modelling tools. The first set of pDT components has been tested on LUMI and the project has established methods for collecting data to be used by the pDTs. For example, over 1 million bird song recordings have been collected via a national-scale citizen science campaign launched in Finland and can be used to identify bird species and model their distribution. Moreover, a recently launched pDT output allow the user to use a browser to interactively calculate pollinators dynamics and productivity in user defined locations via a shiny.app. By combining different modelling methods in new ways and by enabling easier model-user interaction, BioDT is producing predictions of biodiversity shifts in time and space that have not been previously possible to obtain.
Each pDT is expected to rely, as far as possible, on open-access components and data, for example using APIs from Research Infrastructures. The BioDT project has taken significant steps in identifying groups of end-users for each pDT and has set up a community space on the LifeWatch ERIC Community Platform. Discussions are underway on demonstrating how specific pDTs could be linked with Destination Earth Data Lake and key services for promoting open data access in Europe, including the European Open Science Cloud.
BioDT has established 10 prototype DTs (pDTs) that are being developed as the project progresses. The prototypes are grouped around four main topics which are Species responses to environmental change; Dynamics and threats from and for species of policy concern; Species interaction with each other and with humans and Genetically detected Biodiversity. The pDTs cover a broad spectrum of Biodiversity subtopics, from grassland productivity and diversity according to environmental conditions and management strategies; to population dynamics and honey production of bees; to the cultural value of biodiversity and to identifying locations of potential climate-resilient wild crop relatives occurrances.
The digital twins designed in BioDT are made of several components and include, for example, features for moving data and feeding them to modelling tools. The first set of pDT components has been tested on LUMI and the project has established methods for collecting data to be used by the pDTs. For example, over 1 million bird song recordings have been collected via a national-scale citizen science campaign launched in Finland and can be used to identify bird species and model their distribution. Moreover, a recently launched pDT output allow the user to use a browser to interactively calculate pollinators dynamics and productivity in user defined locations via a shiny.app. By combining different modelling methods in new ways and by enabling easier model-user interaction, BioDT is producing predictions of biodiversity shifts in time and space that have not been previously possible to obtain.
Each pDT is expected to rely, as far as possible, on open-access components and data, for example using APIs from Research Infrastructures. The BioDT project has taken significant steps in identifying groups of end-users for each pDT and has set up a community space on the LifeWatch ERIC Community Platform. Discussions are underway on demonstrating how specific pDTs could be linked with Destination Earth Data Lake and key services for promoting open data access in Europe, including the European Open Science Cloud.
Given the innovative nature of BioDT to investigate DTs for biodiversity modelling, the project relies on an iterative approach in which prototype DTs are further refined based on project requirements and end-user feedback. In these first two years, the pDTs under development in BioDT are demonstrating multiple feasible ways in which the digital twin concept can be applied to the Biodiversity field. The feedback gathered is being accounted for third year of the project, and will contribute toward the successful uptake of the pDTs by ensuring their alignment with end-user needs and expectations.
The BioDT project has identified several key needs in advancing FAIR principles (findability, accessibility, interoperability and reusability) in relation to biodiversity data. Through pioneering work on FAIR-compliant DTs, the project seeks to facilitate further work in this field through connecting DTs with data supplied through European biodiversity research infrastructures.
The BioDT project has identified several key needs in advancing FAIR principles (findability, accessibility, interoperability and reusability) in relation to biodiversity data. Through pioneering work on FAIR-compliant DTs, the project seeks to facilitate further work in this field through connecting DTs with data supplied through European biodiversity research infrastructures.