Implementation of the Virtual Research environment for the Earth’s Critical Zone within the ITINERIS PNRR project

Environmental Modeling and Data Management

The Critical Zone (CZ) VRE, developed as part of the ITINERIS PNRR project, aims to create a collaborative research environment for scientists studying the Earth's Critical Zone. The CZ is a complex and dynamic system that encompasses the Earth's surface and near-surface environment, where interactions between rocks, soil, water, air, and living organisms occur. 

The CZ VRE leverages the D4Science platform to integrate data from various Critical Zone Observatories (CZOs) in Italy and internationally. This data integration allows researchers to access and analyze information from diverse sources, facilitating a more comprehensive understanding of CZ processes.

Implementation of the Virtual Research environment for the Earth’s Critical Zone within the ITINERIS PNRR project

Advantages Provided by D4Science

1. Data Integration and Accessibility

The primary services offered by the CZ VRE and implemented by D4Science are an online environment offering large computing capabilities, a shareable folder system, and a social networking system. The VRE is equipped with an area for data collection with a Collaborative Storage Framework and a collaborative experimental space that promotes teamwork and offers the opportunity to share digital objects. In particular, the Workspace is a reliable, distributed, online file system that allows a VRE member to upload files, create private folders, share folders with specific colleagues, publish folders, share data, and directly publish data in a catalogue. 

2. Advanced Analytical Tools

The CZ VRE contains different types of products, including codes in different programming languages (e.g., R and Python), open-source applications and models (e.g., Maxent, OGGM) and web applications for creating and sharing computational documents (e.g., Jupyter Notebook). D4Science offers both the DataMiner service to integrate algorithms directly on the VRE, the RStudio development environment to develop algorithms, and also allows to develop python and Jupyter notebooks. 

3. Collaborative Environment

The social networking board system integrated into the VRE by D4Science allows the exchange of messages between users. The board for open discussions allows to share updates, links and files from the VRE folders and directly mention other participants or tag topics and keywords. Members of the VRE can also reply to a specific post or add a “Like” as reaction. The VRE members can also set specific options to receive notifications (via email and/or the ITINERIS VRE Gateway) on the social activities and the workspace and catalogue uploads. 

4. Metadata Creation and Publication

D4Science offer a Metadata Catalogue for geospatial data, based on GeoNetwork. GeoNetwork is an open-source application devoted to managing and searching spatially referenced resources. All metadata hosted in the CZ VRE are compliant with descriptive standards, i.e. those of the INSPIRE (Infrastructure for Spatial Information in Europe) Directive, and the ISO19139 XML scheme implementation.

Scientific Perspective

The Critical Zone (CZ) represents the thin layer between the unweathered bedrock and the top of the vegetation canopy where “rock meets life”. Therefore, the CZ includes soil, water, microbiota, vegetation and fauna, the services they provide to mankind, all the processes supporting terrestrial ecosystems and the soil-vegetation-atmosphere interactions. As such, the CZ is a fully trans-disciplinary topic which needs to be collectively addressed by a network of intercommunicating observatories providing shared models. A Virtual Research Environment (VRE) is an e-Science environment built to support the principles of Open Science and data FAIRness (data which meet the principles of findability, accessibility, interoperability, and reusability). The goal of a VRE is to enhance collaboration among researchers to find appropriate solutions and address specific scientific and/or management questions. Modelling the CZ through a VRE is natural, because the VRE allows to implement a network of intercommunicating scientists and data sources.

Impact

The main stakeholders of the CZ VRE were identified as conservationists and managers of protected areas, together with the scientific community interested in the analysis of the complex processes involved in the CZ dynamics. The main sources (in terms of data and metadata) feeding the CZ VRE are the IGG-CNR Critical Zone Observatories which provide measurements from automated and portable accumulation chambers and Eddy covariance stations, and data from instrumentation deployed by specific projects such as IDROCZ and WinterCZ. Also, the Copernicus and MODIS services provide metadata and data acquisition procedures. The VRE currently hosts high-impact data, listed in the following. The variables measured by IGG-CNR across different environments and locations and currently available in the CZ VRE are: 

  • The Arctic (Ny Ålesund): CO2 flux, vegetation class, atmospheric pressure, soil volumetric water content, soil temperature, air temperature, air relative humidity, solar irradiance, green fractional cover; 
  • Pianosa: CO2 flux, atmospheric pressure, soil volumetric water content, soil temperature, air temperature, air relative humidity, wind direction, wind speed, rain gauge 
  • Lauson: CO2 flux, atmospheric pressure, soil volumetric water content, soil temperature, air temperature, air relative humidity, solar irradiance 
  • Lavassey: CO2 flux, atmospheric pressure, soil volumetric water content, soil temperature, air temperature, air relative humidity, solar irradiance 
  • Forni: CO2 flux, atmospheric pressure, soil volumetric water content, soil temperature, air temperature, air relative humidity, solar irradiance 
  • Nivolet: CO2 flux, atmospheric pressure, soil volumetric water content, soil temperature, air temperature, air relative humidity, solar irradiance, Eddy covariance The code and software currently available in the CZ VRE are: 
  • Glacier outlines (in Python): OGGM – Open Global Glacier Model (Maussion et al., 2019); High-res prediction of soil temperature in proglacial areas 
  • Eddy covariance (in R): Visualization of time series of CO2 fluxes and environmental variables 
  • Portable chambers (in R): Non-linear modelling of CO2 fluxes; Visualization of spatial trends in CO2 fluxes and environmental variables 
  • Automated chambers (in R): Smoothing and visualization of time series of CO2 fluxes 
  • Data Miner (as-a-service): Bayesian Methods; Feed Forward Neural Network Trainer and Regressor; Habitat Representativeness Score; BIMAC; Support Vector Machines Modelling; Occurrences Obis Data Retrieval 
  • Notebook (in Python): Interactive tools for data visualization and processing 
     


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