2025
Journal article
Restricted
NAVIGATOR: a regional multimodal imaging biobank initiative powered by AI tools for precision medicine in oncology
Aghakhanyan G., Barucci A., Pascali M. A., Assante M., Bagnacci G., Bertelli E., Caputo F. P., Cuibari M. E., Carlini E., Carpi R., Caudai C., Cioni D., Colantonio S., Colcelli V., Dell'Amico A., Vecchio V. D., Gangi D. D., Faggioni L., Formica V., Francischello R., Frosini L., Kotsa C., Lipari G., Manghi P., Martino V. D., Marzi C., Mazzei M. A., Mangiacrapa F., Meglio N. D., Miele V., Molinaro E., Paiar F., Pagano P., Panichi G., Pasquinelli F., Peccerillo B., Perrella A., Piccioli T., Oliviero A., Olivoni M., Rucci D., Tampucci M., Tumminello L., Volpini F., Zanuzzi A., Fanni S. C., Neri E.
The NAVIGATOR project established an Italian regional imaging biobank and interactive research platform designed to support precision oncology through the integration of multimodal imaging, clinical, and omics data. The platform goes beyond a static repository, offering a secure Virtual Research Environment (VRE) where users can upload data, test AI algorithms, and execute complete analytical pipelines. The platform incorporates artificial intelligence (AI)-driven radiomics and deep learning methodologies to enable biomarker extraction, disease stratification, and predictive modeling. This manuscript presents the development and implementation of the NAVIGATOR infrastructure, including its data governance framework, ethical and legal considerations, and application to three oncological use cases: prostate, rectal, and gastric cancers. To date, the biobank has collected imaging and clinical data from over 700 patients across these cohorts. AI models were deployed within a dedicated VRE to facilitate image analysis, feature extraction, and classification tasks. The project addresses critical challenges related to data harmonization, regulatory compliance, privacy safeguards and fairness in AI systems. NAVIGATOR demonstrates the feasibility of integrating AI methodologies within imaging biobanks and provides a scalable framework to advance oncological research and support clinical decision-making.Source: EUROPEAN JOURNAL OF RADIOLOGY, vol. 191 (issue 112327)
DOI: 10.1016/j.ejrad.2025.112327
Project(s): An Imaging Biobank to Precisely Prevent and Predict cancer, and facilitate the Participation of oncologic patients to Diagnosis and Treatment
Metrics:
Aghakhanyan G., Barucci A., Pascali M. A., Assante M., Bagnacci G., Bertelli E., Caputo F. P., Cuibari M. E., Carlini E., Carpi R., Caudai C., Cioni D., Colantonio S., Colcelli V., Dell'Amico A., Vecchio V. D., Gangi D. D., Faggioni L., Formica V., Francischello R., Frosini L., Kotsa C., Lipari G., Manghi P., Martino V. D., Marzi C., Mazzei M. A., Mangiacrapa F., Meglio N. D., Miele V., Molinaro E., Paiar F., Pagano P., Panichi G., Pasquinelli F., Peccerillo B., Perrella A., Piccioli T., Oliviero A., Olivoni M., Rucci D., Tampucci M., Tumminello L., Volpini F., Zanuzzi A., Fanni S. C., Neri E.
The NAVIGATOR project established an Italian regional imaging biobank and interactive research platform designed to support precision oncology through the integration of multimodal imaging, clinical, and omics data. The platform goes beyond a static repository, offering a secure Virtual Research Environment (VRE) where users can upload data, test AI algorithms, and execute complete analytical pipelines. The platform incorporates artificial intelligence (AI)-driven radiomics and deep learning methodologies to enable biomarker extraction, disease stratification, and predictive modeling. This manuscript presents the development and implementation of the NAVIGATOR infrastructure, including its data governance framework, ethical and legal considerations, and application to three oncological use cases: prostate, rectal, and gastric cancers. To date, the biobank has collected imaging and clinical data from over 700 patients across these cohorts. AI models were deployed within a dedicated VRE to facilitate image analysis, feature extraction, and classification tasks. The project addresses critical challenges related to data harmonization, regulatory compliance, privacy safeguards and fairness in AI systems. NAVIGATOR demonstrates the feasibility of integrating AI methodologies within imaging biobanks and provides a scalable framework to advance oncological research and support clinical decision-making.Source: EUROPEAN JOURNAL OF RADIOLOGY, vol. 191 (issue 112327)
DOI: 10.1016/j.ejrad.2025.112327
Project(s): An Imaging Biobank to Precisely Prevent and Predict cancer, and facilitate the Participation of oncologic patients to Diagnosis and Treatment
Metrics:
See at:
European Journal of Radiology 
| Archivio della Ricerca - Università di Pisa | CNR IRIS | CNR IRIS | Archivio della Ricerca - Università di Pisa
2025
Other
Restricted
InfraScience research activity report 2024
Angioni S., Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Bosio C., Bove P., Calanducci A., Candela L., Casini G., Castelli D., Cirillo R., Coro G., De Bonis M., Debole F., Dell'Amico A., Frosini L., Ibrahim Ahmed, La Bruzzo S., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Molinaro E., Oliviero A., Pagano P., Panichi G., Teresa M. T., Pavone G., Peccerillo B., Piccioli T., Procaccini M., Straccia U., Vannini G. L., Versienti L.
InfraScience is a research group within the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR), based in Pisa. This activity report outlines the group's research achievements and initiatives throughout 2024. InfraScience focused its efforts on key challenges in the areas of Data Infrastructures, e-Science, and Intelligent Systems, maintaining a strong synergy between research and development and a firm commitment to open science principles. In 2024, the group played a leading role in the development and evolution of two major Open Science infrastructures: D4Science and OpenAIRE. InfraScience researchers contributed significantly to the scientific community through the publication of peer-reviewed papers, active participation in EU-funded research projects, organization of international conferences and training activities, and engagement in various working groups and task forces. This report highlights these contributions and underscores the group's ongoing dedication to advancing open, collaborative, and impactful science.DOI: 10.32079/isti-ar-2025/001
Metrics:
Angioni S., Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Bosio C., Bove P., Calanducci A., Candela L., Casini G., Castelli D., Cirillo R., Coro G., De Bonis M., Debole F., Dell'Amico A., Frosini L., Ibrahim Ahmed, La Bruzzo S., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Molinaro E., Oliviero A., Pagano P., Panichi G., Teresa M. T., Pavone G., Peccerillo B., Piccioli T., Procaccini M., Straccia U., Vannini G. L., Versienti L.
InfraScience is a research group within the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR), based in Pisa. This activity report outlines the group's research achievements and initiatives throughout 2024. InfraScience focused its efforts on key challenges in the areas of Data Infrastructures, e-Science, and Intelligent Systems, maintaining a strong synergy between research and development and a firm commitment to open science principles. In 2024, the group played a leading role in the development and evolution of two major Open Science infrastructures: D4Science and OpenAIRE. InfraScience researchers contributed significantly to the scientific community through the publication of peer-reviewed papers, active participation in EU-funded research projects, organization of international conferences and training activities, and engagement in various working groups and task forces. This report highlights these contributions and underscores the group's ongoing dedication to advancing open, collaborative, and impactful science.DOI: 10.32079/isti-ar-2025/001
Metrics:
2025
Other
Open Access
D4Science interoperability framework: developer guidance for service integration
Assante M., Dell'Amico A., Molinaro E., Oliviero A.
The D4Science Interoperability Framework provides the architectural backbone for integrating and operating heterogeneous services within the D4Science ecosystem. D4Science is a distributed digital infrastructure supporting international research communities through the operation of Virtual Research Environments (VREs) that enable collaborative access to data, analytical tools, and computing resources in line with Open Science and FAIR principles. The framework integrates core components such as the VRE Gateway, Virtual Labs, Identity and Access Management (IAM), and the Analytics Engine to deliver secure, scalable, and reproducible workflows. This document offers detailed guidance for service developers, covering containerisation, orchestration with Docker Swarm, authentication with OpenID Connect and OAuth2, and integrated monitoring and auditing tools. By combining federated access, container based deployment, and robust governance mechanisms, this solution enables developers and researchers to create reusable, interoperable, and compliant services that advance collaborative and transparent scientific research.DOI: 10.32079/isti-tr-2025/015
Metrics:
Assante M., Dell'Amico A., Molinaro E., Oliviero A.
The D4Science Interoperability Framework provides the architectural backbone for integrating and operating heterogeneous services within the D4Science ecosystem. D4Science is a distributed digital infrastructure supporting international research communities through the operation of Virtual Research Environments (VREs) that enable collaborative access to data, analytical tools, and computing resources in line with Open Science and FAIR principles. The framework integrates core components such as the VRE Gateway, Virtual Labs, Identity and Access Management (IAM), and the Analytics Engine to deliver secure, scalable, and reproducible workflows. This document offers detailed guidance for service developers, covering containerisation, orchestration with Docker Swarm, authentication with OpenID Connect and OAuth2, and integrated monitoring and auditing tools. By combining federated access, container based deployment, and robust governance mechanisms, this solution enables developers and researchers to create reusable, interoperable, and compliant services that advance collaborative and transparent scientific research.DOI: 10.32079/isti-tr-2025/015
Metrics:
2024
Other
Open Access
SoBigData++ - SoBigData e-Infrastructure Operation Report 3
Assante M., Candela L., Dell'Amico A., Frosini L., Mangiacrapa F., Molinaro E., Oliviero A., Pagano P., Panichi G., Piccioli T.
This Deliverable builds upon and updates the previous reports, D9.2 - “SoBigData e-Infrastructure Operation Report 2” [5] and D9.1 - “SoBigData e-Infrastructure Operation Report 1” [3]. The SoBigData e-Infrastructure has been pivotal in enabling the core services and research support required for the SoBigData++ project, including Virtual Research Environments (VREs), the Catalogue, and Analytics Services. It is accessible through the SoBigData gateway (https://sobigdata.d4science.org), which provides end-users with seamless access to tools, datasets, and services. The SoBigData e-Infrastructure is built upon the D4Science infrastructure, offering a comprehensive platform that facilitates collaborative, transparent, and interdisciplinary research. The deployment and operation of VREs followed a well-defined procedure, leveraging the consolidated process inherited from D4Science. Throughout the 60 months of the project, a total of 27 VREs were created and operated to meet project and community needs. These VREs were classified into five categories: Exploratories, Applications, Virtual Labs, Training, and Management. Notable examples include, (i) SoBigDataLab and SoBigDataLab-PlusPlus for method development and experiments, (ii) Training VREs created for events like Summer Schools and specialised workshops, and (iii) Research spaces (formerly known as Exploratories) supporting targeted domains, such as Migration Studies, Sports Data Science, and Social Impacts of AI. The SoBigData Catalogue (https://sobigdata.d4science.org/catalogue-sobigdata) emerged as a critical resource for both human users and integrated services, enabling access to datasets, services, and analytical methods. The catalogue supports customisable item profiles enriched with metadata fields, controlled vocabularies, and validation rules. By end of term, the Catalogue recorded significant growth, particularly in key item types such as Methods (192 items) and Datasets (250 items). This expansion underscores the Catalogue’s role in promoting resource discoverability and supporting research workflows. Its usage indicators demonstrate its active adoption, with 31,909 total accesses, 29,595 metadata views, and 4,171 resource views recorded. Monthly trends reveal consistent engagement, highlighting its importance in the research ecosystem. The Social Mining Analytics Engine (SMAE) transitioned through the development of a new service, namely Cloud Computing Platform (CCP), offering enhanced scalability and automation through container orchestrations. Methods hosted on the SMAE span multiple categories, such as Text Processing, Web Analytics, and Image Analysis. Over the last year, the platform executed an average of 6.4 million method invocations per month, peaking at 16 million executions in July 2024. As of mid-December ’24, the e-infrastructure serves more than 13,000 users, with an overall trend in the use of the SoBigData VREs from January 2020 to December 2024, highlighting their importance for the research community. The steady engagement through 2023 and 2024, with peaks like July 2024 (2,592 sessions), underscores the VREs continued relevance and utility.Project(s): SoBigData-PlusPlus
Assante M., Candela L., Dell'Amico A., Frosini L., Mangiacrapa F., Molinaro E., Oliviero A., Pagano P., Panichi G., Piccioli T.
This Deliverable builds upon and updates the previous reports, D9.2 - “SoBigData e-Infrastructure Operation Report 2” [5] and D9.1 - “SoBigData e-Infrastructure Operation Report 1” [3]. The SoBigData e-Infrastructure has been pivotal in enabling the core services and research support required for the SoBigData++ project, including Virtual Research Environments (VREs), the Catalogue, and Analytics Services. It is accessible through the SoBigData gateway (https://sobigdata.d4science.org), which provides end-users with seamless access to tools, datasets, and services. The SoBigData e-Infrastructure is built upon the D4Science infrastructure, offering a comprehensive platform that facilitates collaborative, transparent, and interdisciplinary research. The deployment and operation of VREs followed a well-defined procedure, leveraging the consolidated process inherited from D4Science. Throughout the 60 months of the project, a total of 27 VREs were created and operated to meet project and community needs. These VREs were classified into five categories: Exploratories, Applications, Virtual Labs, Training, and Management. Notable examples include, (i) SoBigDataLab and SoBigDataLab-PlusPlus for method development and experiments, (ii) Training VREs created for events like Summer Schools and specialised workshops, and (iii) Research spaces (formerly known as Exploratories) supporting targeted domains, such as Migration Studies, Sports Data Science, and Social Impacts of AI. The SoBigData Catalogue (https://sobigdata.d4science.org/catalogue-sobigdata) emerged as a critical resource for both human users and integrated services, enabling access to datasets, services, and analytical methods. The catalogue supports customisable item profiles enriched with metadata fields, controlled vocabularies, and validation rules. By end of term, the Catalogue recorded significant growth, particularly in key item types such as Methods (192 items) and Datasets (250 items). This expansion underscores the Catalogue’s role in promoting resource discoverability and supporting research workflows. Its usage indicators demonstrate its active adoption, with 31,909 total accesses, 29,595 metadata views, and 4,171 resource views recorded. Monthly trends reveal consistent engagement, highlighting its importance in the research ecosystem. The Social Mining Analytics Engine (SMAE) transitioned through the development of a new service, namely Cloud Computing Platform (CCP), offering enhanced scalability and automation through container orchestrations. Methods hosted on the SMAE span multiple categories, such as Text Processing, Web Analytics, and Image Analysis. Over the last year, the platform executed an average of 6.4 million method invocations per month, peaking at 16 million executions in July 2024. As of mid-December ’24, the e-infrastructure serves more than 13,000 users, with an overall trend in the use of the SoBigData VREs from January 2020 to December 2024, highlighting their importance for the research community. The steady engagement through 2023 and 2024, with peaks like July 2024 (2,592 sessions), underscores the VREs continued relevance and utility.Project(s): SoBigData-PlusPlus
2023
Other
Open Access
InfraScience research activity report 2023
Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Bosio C., Bove P., Calanducci A., Candela L., Casini G., Castelli D., Cirillo R., Coro G., De Bonis M., Debole F., Dell'Amico A., Frosini L., Ibrahim A. S. T., La Bruzzo S., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Molinaro E., Pagano P., Panichi G., Paratore M. T., Pavone G., Piccioli T., Sinibaldi F., Straccia U., Vannini G. L.
InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2023 to highlight the major results. In particular, the InfraScience group engaged in research challenges characterising Data Infrastructures, e-Science, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2023 InfraScience members contributed to the publishing of several papers, to the research and development activities of several research projects (primarily funded by EU), to the organization of conferences and training events, to several working groups and task forces.DOI: 10.32079/isti-ar-2023/002
Project(s): Blue Cloud, EOSC Future , TAILOR
Metrics:
Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Bosio C., Bove P., Calanducci A., Candela L., Casini G., Castelli D., Cirillo R., Coro G., De Bonis M., Debole F., Dell'Amico A., Frosini L., Ibrahim A. S. T., La Bruzzo S., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Molinaro E., Pagano P., Panichi G., Paratore M. T., Pavone G., Piccioli T., Sinibaldi F., Straccia U., Vannini G. L.
InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2023 to highlight the major results. In particular, the InfraScience group engaged in research challenges characterising Data Infrastructures, e-Science, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2023 InfraScience members contributed to the publishing of several papers, to the research and development activities of several research projects (primarily funded by EU), to the organization of conferences and training events, to several working groups and task forces.DOI: 10.32079/isti-ar-2023/002
Project(s): Blue Cloud
, EOSC Future , TAILOR Metrics:
2023
Other
Open Access
DESIRA D5.3 - Virtual Research Environment operation report years 3-4
Assante M, Candela L, Cirillo R, Dell'Amico A, Frosini L, Lelii L, Mangiacrapa F, Pagano P, Panichi G, Piccioli T
This deliverable D5.3 "Virtual Research Environment Operation Report years 3-4" is the revised and updated version of deliverable D5.2 "Virtual Research Environment Operation Report years 1-2". It describes the activities carried out during the DESIRA project within Work Package 5. Specifically, in Task 5.1 "Knowledge Infrastructure: the DESIRA Virtual Research Environment" and Task 5.2 "Integration of Services and Tools and Use Reporting". It reports the procedures governing the operation of the VREs as well as the status of the aggregated resources at the end of the project in the DESIRA infrastructure. Virtual Research Environments (VREs) are "systems" specifically conceived to provide their users with a web-based set of facilities (including services, data and computational facilities) to accomplish a set of tasks by dynamically relying on the underlying infrastructure. VREs are among the key products to be developed and delivered by the DESIRA project to support Project coordination, Living Labs activities and Rural Digitization Forums activities. The development of VREs is based on three main activities: (i) the development of software artefacts that realise a set of functions (including those needed for accessing specific datasets), (ii) the deployment of these artefacts in an operational infrastructure following the release procedures and tools, and (iii) the final deployment and operation of well-defined Virtual Research Environments by exploiting the facilities offered by the underlying D4Science infrastructure and its services [1, 2]. This report documents the last of the above three activities - i.e. the exploitation of the services and technologies offered by the underlying infrastructure to serve the needs of defined scenarios - as implemented in the context of the DESIRA project. The DESIRA Infrastructure Gateway offers end-user access to 14 VREs. As of May 2023, 14 VREs were created and operated. Specifically, the DESIRA Project VRE (cf. Sec 3.1.1) was created before the project kick-off. These VREs have served the needs of more than 390 users and more than 10.200 user sessions. This required dealing with 185 tickets (121 related to the project management, 43 requests for tasks, support and enhancements; 7 requests for incidents and bugs; 14 requests for VRE creations).Project(s): DESIRA
Assante M, Candela L, Cirillo R, Dell'Amico A, Frosini L, Lelii L, Mangiacrapa F, Pagano P, Panichi G, Piccioli T
This deliverable D5.3 "Virtual Research Environment Operation Report years 3-4" is the revised and updated version of deliverable D5.2 "Virtual Research Environment Operation Report years 1-2". It describes the activities carried out during the DESIRA project within Work Package 5. Specifically, in Task 5.1 "Knowledge Infrastructure: the DESIRA Virtual Research Environment" and Task 5.2 "Integration of Services and Tools and Use Reporting". It reports the procedures governing the operation of the VREs as well as the status of the aggregated resources at the end of the project in the DESIRA infrastructure. Virtual Research Environments (VREs) are "systems" specifically conceived to provide their users with a web-based set of facilities (including services, data and computational facilities) to accomplish a set of tasks by dynamically relying on the underlying infrastructure. VREs are among the key products to be developed and delivered by the DESIRA project to support Project coordination, Living Labs activities and Rural Digitization Forums activities. The development of VREs is based on three main activities: (i) the development of software artefacts that realise a set of functions (including those needed for accessing specific datasets), (ii) the deployment of these artefacts in an operational infrastructure following the release procedures and tools, and (iii) the final deployment and operation of well-defined Virtual Research Environments by exploiting the facilities offered by the underlying D4Science infrastructure and its services [1, 2]. This report documents the last of the above three activities - i.e. the exploitation of the services and technologies offered by the underlying infrastructure to serve the needs of defined scenarios - as implemented in the context of the DESIRA project. The DESIRA Infrastructure Gateway offers end-user access to 14 VREs. As of May 2023, 14 VREs were created and operated. Specifically, the DESIRA Project VRE (cf. Sec 3.1.1) was created before the project kick-off. These VREs have served the needs of more than 390 users and more than 10.200 user sessions. This required dealing with 185 tickets (121 related to the project management, 43 requests for tasks, support and enhancements; 7 requests for incidents and bugs; 14 requests for VRE creations).Project(s): DESIRA
See at:
CNR IRIS 
| ISTI Repository | CNR IRIS
2023
Other
Open Access
SoBigData.it D1.2 - Plan for the acquisition and installation of new computational resources
Pagano P, Assante M, Cirillo R, Dell'Amico A, Molinaro E, Piccioli T, Silvestri S, Passarella A, Bruno R, Cicconetti C, Davini M, Di Marco A, Di Pompeo D, Stilo G, Tucci M, Croce D, Palazzo S, Schembra G, Bujari A, Bellavista P, Virone G, Greco E, Gentile Af
The SoBigData Research Infrastructure (RI) has the ambition to support the rising demand for cross- disciplinary research and innovation on the multiple aspects of social complexity from combined data and model-driven perspectives and the increasing importance of ethics and data scientists' responsibility as a pillar of trustworthy use of Big Data and analytical technology. Digital traces of human activities offer a considerable opportunity to scrutinise the ground truth of individual and collective behaviour at an unprecedented detail and on a global scale. Work Package 1 (WP1) focuses on the creation of computational nodes within the SoBigData RI by connecting data centres to the RI network. This initiative aims to enhance the RI storage and computing capabilities, ensuring both short and long-term scalability, robustness, availability, and reliability of services. Furthermore, it integrates state-of-the-art nodes in the domains of pervasive computing and networking, as well as beyond 5G networks. These nodes are built using the latest-generation architectures and technologies, encompassing edge and far-edge devices, the Internet of Things (IoT), and next-generation networks. By adopting this comprehensive approach, SoBigData provides access to state-of-the-art data centres while embracing advanced solutions for decentralised data centres of the future. This decentralised infrastructure spans from the cloud to the network periphery, forming a continuum of distributed data processing and networking resources. This Deliverable documents the plan for the acquisition and installation of new computational resources. The deliverable consists of 5 sections: Section 1 briefly introduces the role of this deliverable and highlights the composition of the infrastructure and its organisation in a multi-site, comprising central and peripheral sites. Sections 2, 3, and 4 provide detailed plans for the acquisition and installation of computational and hardware resources related to green data centres, pervasive computing, and beyond 5G networks. Specifically, Section 2 outlines the plan for green data centres. Section 3 focuses on the plan for pervasive computing and networking nodes. Section 4 details the plan for implementing the architectural framework of the infrastructure representing the beyond 5G node. Finally the report concludes with Section 5.
Pagano P, Assante M, Cirillo R, Dell'Amico A, Molinaro E, Piccioli T, Silvestri S, Passarella A, Bruno R, Cicconetti C, Davini M, Di Marco A, Di Pompeo D, Stilo G, Tucci M, Croce D, Palazzo S, Schembra G, Bujari A, Bellavista P, Virone G, Greco E, Gentile Af
The SoBigData Research Infrastructure (RI) has the ambition to support the rising demand for cross- disciplinary research and innovation on the multiple aspects of social complexity from combined data and model-driven perspectives and the increasing importance of ethics and data scientists' responsibility as a pillar of trustworthy use of Big Data and analytical technology. Digital traces of human activities offer a considerable opportunity to scrutinise the ground truth of individual and collective behaviour at an unprecedented detail and on a global scale. Work Package 1 (WP1) focuses on the creation of computational nodes within the SoBigData RI by connecting data centres to the RI network. This initiative aims to enhance the RI storage and computing capabilities, ensuring both short and long-term scalability, robustness, availability, and reliability of services. Furthermore, it integrates state-of-the-art nodes in the domains of pervasive computing and networking, as well as beyond 5G networks. These nodes are built using the latest-generation architectures and technologies, encompassing edge and far-edge devices, the Internet of Things (IoT), and next-generation networks. By adopting this comprehensive approach, SoBigData provides access to state-of-the-art data centres while embracing advanced solutions for decentralised data centres of the future. This decentralised infrastructure spans from the cloud to the network periphery, forming a continuum of distributed data processing and networking resources. This Deliverable documents the plan for the acquisition and installation of new computational resources. The deliverable consists of 5 sections: Section 1 briefly introduces the role of this deliverable and highlights the composition of the infrastructure and its organisation in a multi-site, comprising central and peripheral sites. Sections 2, 3, and 4 provide detailed plans for the acquisition and installation of computational and hardware resources related to green data centres, pervasive computing, and beyond 5G networks. Specifically, Section 2 outlines the plan for green data centres. Section 3 focuses on the plan for pervasive computing and networking nodes. Section 4 details the plan for implementing the architectural framework of the infrastructure representing the beyond 5G node. Finally the report concludes with Section 5.
2023
Other
Open Access
SoBigData-PlusPlus D9.2 - SoBigData e-Infrastructure Operation Report 2
Assante M, Candela L, Cirillo R, Dell'Amico A, Frosini L, Lelii L, Mangiacrapa F, Pagano P, Panichi G, Piccioli T
This Deliverable D9.2 - "SoBigData e-Infrastructure Operation Report 2" is the revised version of the deliverable D9.1 - "SoBigData e-Infrastructure Operation Report 1" [3]. It reports on the activities carried out within Work Package 9 in the period from M19 (January 2021) to M36 (December 2022) for the SoBigData e- Infrastructure operation activity. It includes a detailed set of usage indicators (i.e., the number of users, access to resources, usage of resources from scientists, etc.). It also reports the deployment and procedures governing the operation of the Virtual Research Environments, the catalogue, and the services devoted to data analytics. A total of 17 Virtual Research Environments (VREs) have been created and/or operated to serve the needs arising in the context of the project. The SoBigData gateway (https://sobigdata.d4science.org/) provide its users with: 6 Exploratories VREs paired with the use cases (Demography, Economy & Finance 2.0; Migration Studies; Societal Debates and Misinformation Analysis; Social Impacts of AI and Explainable Machine Learning; Sports Data Science; Sustainable Cities for Citizens); 4 Virtual Lab VREs - SoBigDataLab and the OpenScienceGraphLab to exploit and experiment tools and solutions, the SoBigData-PlusPlus at DSAA 2021 Lab and the XAISS VLab, conceived to be the working environment for Hands-on Tutorials showing the services provided by SoBigData for the new generation of Responsible data scientists; 3 Applications VREs - TagME, SMAPH, M-Atlas; 2 Project Internal VREs - SoBigData.eu VRE for the communications and collaboration among project and initiative members and SBD-InfraCore VRE for supporting SoBigData++ WP9; 2 Literacy And Training VREs - the SoBigDataLiteracy, supporting Critical Data Literacy of task T.2.4, creating a curated collection of literature of interest for the SoBigData Community, and the e-Learning_Area VRE to host training materials developed within the SoBigData project. As of mid-December 2022, the e-infrastructure served more than 10,000 users by a total of more than 47,000 working sessions, with an average of 1350 working sessions per month with stable trend. This required to deal with approximately 130 issue tracker tickets (65 requests for support, 4 requests for incidents and bugs, 22 requests for new features, and 39 requests for Tasks, Virtual Machine or Container creations).Project(s): SoBigData-PlusPlus
Assante M, Candela L, Cirillo R, Dell'Amico A, Frosini L, Lelii L, Mangiacrapa F, Pagano P, Panichi G, Piccioli T
This Deliverable D9.2 - "SoBigData e-Infrastructure Operation Report 2" is the revised version of the deliverable D9.1 - "SoBigData e-Infrastructure Operation Report 1" [3]. It reports on the activities carried out within Work Package 9 in the period from M19 (January 2021) to M36 (December 2022) for the SoBigData e- Infrastructure operation activity. It includes a detailed set of usage indicators (i.e., the number of users, access to resources, usage of resources from scientists, etc.). It also reports the deployment and procedures governing the operation of the Virtual Research Environments, the catalogue, and the services devoted to data analytics. A total of 17 Virtual Research Environments (VREs) have been created and/or operated to serve the needs arising in the context of the project. The SoBigData gateway (https://sobigdata.d4science.org/) provide its users with: 6 Exploratories VREs paired with the use cases (Demography, Economy & Finance 2.0; Migration Studies; Societal Debates and Misinformation Analysis; Social Impacts of AI and Explainable Machine Learning; Sports Data Science; Sustainable Cities for Citizens); 4 Virtual Lab VREs - SoBigDataLab and the OpenScienceGraphLab to exploit and experiment tools and solutions, the SoBigData-PlusPlus at DSAA 2021 Lab and the XAISS VLab, conceived to be the working environment for Hands-on Tutorials showing the services provided by SoBigData for the new generation of Responsible data scientists; 3 Applications VREs - TagME, SMAPH, M-Atlas; 2 Project Internal VREs - SoBigData.eu VRE for the communications and collaboration among project and initiative members and SBD-InfraCore VRE for supporting SoBigData++ WP9; 2 Literacy And Training VREs - the SoBigDataLiteracy, supporting Critical Data Literacy of task T.2.4, creating a curated collection of literature of interest for the SoBigData Community, and the e-Learning_Area VRE to host training materials developed within the SoBigData project. As of mid-December 2022, the e-infrastructure served more than 10,000 users by a total of more than 47,000 working sessions, with an average of 1350 working sessions per month with stable trend. This required to deal with approximately 130 issue tracker tickets (65 requests for support, 4 requests for incidents and bugs, 22 requests for new features, and 39 requests for Tasks, Virtual Machine or Container creations).Project(s): SoBigData-PlusPlus
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2023
Other
Open Access
Blue-Cloud2026 D5.1 - Blue-Cloud VRE Common Services 1st Release
Assante M, Candela L, Cirillo R, Dell'Amico A, Fernandez E, Frosini L, Lelii L, Lettere M, Mangiacrapa F, Pagano P, Panichi G, Piccioli T
This deliverable document the design principles and software architecture characterising the release and development of the Blue-Cloud Virtual Research Environment (VRE) common services, namely the analytics computing framework, the catalogue framework, the storage framework and the enabling framework components. This report is the first of two versions, each one describing the design associated with a specific version of the VRE. This deliverable focuses on the design principles and software architecture included in the first release of ththis one as released at M12 (December 2023), while a second release is due at the end of the third year of the project and will be reported in D5.4 Blue-Cloud VRE Common Services 2nd Release (M36), due in December 2025. The deliverable consists of six sections. ? Section 1 briefly introduces the role of this deliverable in the development and delivery of the Blue-Cloud VRE common services. ? Section 2 describes the Blue-Cloud VRE logical architecture of the common services and how they relate to the other services available in the VRE. ? Section 3, 4, 5 and 6 document the first release of the Blue-Cloud VRE common services available at M12, reporting the design principles and reference software architecture of the released solutions. Specifically, Section 3 describes the analytics computing framework which includes the Analytics Engine, the RStudio and the Jupyter Notebooks via JupyterHub. Section 4 presents the VRE Catalogue framework and its components, and section 5 reports on the Storage framework. ? Finally, section 6 concludes the report by illustrating the services composing the Enabling framework, which is used as a common ground for all the above-mentioned frameworks.
Assante M, Candela L, Cirillo R, Dell'Amico A, Fernandez E, Frosini L, Lelii L, Lettere M, Mangiacrapa F, Pagano P, Panichi G, Piccioli T
This deliverable document the design principles and software architecture characterising the release and development of the Blue-Cloud Virtual Research Environment (VRE) common services, namely the analytics computing framework, the catalogue framework, the storage framework and the enabling framework components. This report is the first of two versions, each one describing the design associated with a specific version of the VRE. This deliverable focuses on the design principles and software architecture included in the first release of ththis one as released at M12 (December 2023), while a second release is due at the end of the third year of the project and will be reported in D5.4 Blue-Cloud VRE Common Services 2nd Release (M36), due in December 2025. The deliverable consists of six sections. ? Section 1 briefly introduces the role of this deliverable in the development and delivery of the Blue-Cloud VRE common services. ? Section 2 describes the Blue-Cloud VRE logical architecture of the common services and how they relate to the other services available in the VRE. ? Section 3, 4, 5 and 6 document the first release of the Blue-Cloud VRE common services available at M12, reporting the design principles and reference software architecture of the released solutions. Specifically, Section 3 describes the analytics computing framework which includes the Analytics Engine, the RStudio and the Jupyter Notebooks via JupyterHub. Section 4 presents the VRE Catalogue framework and its components, and section 5 reports on the Storage framework. ? Finally, section 6 concludes the report by illustrating the services composing the Enabling framework, which is used as a common ground for all the above-mentioned frameworks.
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2023
Other
Restricted
TerritoriAperti - Report a 30 mesi
Assante M., Pagano P., Dell'Amico A., Cirillo R., Mangiacrapa F., Frosini L., Panichi G.
The Territori Aperti Gateway1, provides users with access to the Territori Aperti Catalogue and to the Exploratories supporting scientific research with the creation of new knowledge and skills through the management and enhancement of data and analytical processes.This document illustrates the services exploited by the Territori Aperti Gateway and reports the status of the activities at the end of the 30 months.
Assante M., Pagano P., Dell'Amico A., Cirillo R., Mangiacrapa F., Frosini L., Panichi G.
The Territori Aperti Gateway1, provides users with access to the Territori Aperti Catalogue and to the Exploratories supporting scientific research with the creation of new knowledge and skills through the management and enhancement of data and analytical processes.This document illustrates the services exploited by the Territori Aperti Gateway and reports the status of the activities at the end of the 30 months.
2023
Other
Restricted
OpenASFA - Final report
Assante M., Cirillo R., Dell'Amico A., Pagano P., Panichi G., Piccioli T.
This document describes the services exploited by the Open-ASFA Virtual Research Environment (OPEN-ASFA VRE) at final term, 30 April 2023. It reports on service availability, maintenance, service operation, upgrades and validation. This report also includes metrics of usage of the various services by ASFA users.
Assante M., Cirillo R., Dell'Amico A., Pagano P., Panichi G., Piccioli T.
This document describes the services exploited by the Open-ASFA Virtual Research Environment (OPEN-ASFA VRE) at final term, 30 April 2023. It reports on service availability, maintenance, service operation, upgrades and validation. This report also includes metrics of usage of the various services by ASFA users.
2022
Journal article
Open Access
Virtual research environments co-creation: the D4Science experience
Assante M, Candela L, Castelli D, Cirillo R, Coro G, Dell'Amico A, Frosini L, Lelii L, Lettere M, Mangiacrapa F, Pagano P, Panichi G, Piccioli T, Sinibaldi F
Virtual research environments are systems called to serve the needs of their designated communities of practice. Every community of practice is a group of people dynamically aggregated by the willingness to collaborate to address a given research question. The virtual research environment provides its users with seamless access to the resources of interest (namely, data and services) no matter what and where they are. Developing a virtual research environment thus to guarantee its uptake from the community of practice is a challenging task. In this article, we advocate how the co-creation driven approach promoted by D4Science has proven to be effective. In particular, we present the co-creation options supported, discuss how diverse communities of practice have exploited these options, and give some usage indicators on the created VREs.Source: CONCURRENCY AND COMPUTATION (ONLINE)
DOI: 10.1002/cpe.6925
Project(s): AGINFRA PLUS, Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus
Metrics:
Assante M, Candela L, Castelli D, Cirillo R, Coro G, Dell'Amico A, Frosini L, Lelii L, Lettere M, Mangiacrapa F, Pagano P, Panichi G, Piccioli T, Sinibaldi F
Virtual research environments are systems called to serve the needs of their designated communities of practice. Every community of practice is a group of people dynamically aggregated by the willingness to collaborate to address a given research question. The virtual research environment provides its users with seamless access to the resources of interest (namely, data and services) no matter what and where they are. Developing a virtual research environment thus to guarantee its uptake from the community of practice is a challenging task. In this article, we advocate how the co-creation driven approach promoted by D4Science has proven to be effective. In particular, we present the co-creation options supported, discuss how diverse communities of practice have exploited these options, and give some usage indicators on the created VREs.Source: CONCURRENCY AND COMPUTATION (ONLINE)
DOI: 10.1002/cpe.6925
Project(s): AGINFRA PLUS
, Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus Metrics:
See at:
CNR IRIS | onlinelibrary.wiley.com | ISTI Repository | CNR IRIS | CNR IRIS
2022
Other
Open Access
InfraScience research activity report 2021
Artini M, Assante M, Atzori C, Baglioni M, Bardi A, Bove P, Candela L, Casini G, Castelli D, Cirillo R, Coro G, De Bonis M, Debole F, Dell'Amico A, Frosini L, La Bruzzo S, Lazzeri E, Lelii L, Manghi P, Mangiacrapa F, Mangione D, Mannocci A, Ottonello E, Pagano P, Panichi G, Pavone G, Piccioli T, Sinibaldi F, Straccia U
InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2021 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, eScience, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2021 InfraScience members contributed to the publishing of 25 papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.DOI: 10.32079/isti-ar-2022/001
Project(s): ARIADNEplus, Blue Cloud , PerformFISH , EOSC-Pillar , DESIRA , EOSC Future , EOSCsecretariat.eu , EcoScope , RISIS 2 , OpenAIRE-Advance , OpenAIRE Nexus , SoBigData-PlusPlus
Metrics:
Artini M, Assante M, Atzori C, Baglioni M, Bardi A, Bove P, Candela L, Casini G, Castelli D, Cirillo R, Coro G, De Bonis M, Debole F, Dell'Amico A, Frosini L, La Bruzzo S, Lazzeri E, Lelii L, Manghi P, Mangiacrapa F, Mangione D, Mannocci A, Ottonello E, Pagano P, Panichi G, Pavone G, Piccioli T, Sinibaldi F, Straccia U
InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2021 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, eScience, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2021 InfraScience members contributed to the publishing of 25 papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.DOI: 10.32079/isti-ar-2022/001
Project(s): ARIADNEplus
, Blue Cloud , PerformFISH , EOSC-Pillar , DESIRA , EOSC Future , EOSCsecretariat.eu , EcoScope , RISIS 2 , OpenAIRE-Advance , OpenAIRE Nexus , SoBigData-PlusPlus Metrics:
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2022
Journal article
Open Access
NAVIGATOR: an Italian regional imaging biobank to promote precision medicine for oncologic patients
Borgheresi R, Barucci A, Colantonio S, Aghakhanyan G, Assante M, Bertelli E, Carlini E, Carpi R, Caudai C, Cavallero D, Cioni D, Cirillo R, Colcelli V, Dell'Amico A, Di Gangi D, Erba Pa, Faggioni L, Falaschi Z, Gabelloni M, Gini R, Lelii L, Liò P, Lorito A, Lucarini S, Manghi P, Mangiacrapa F, Marzi C, Mazzei Ma, Mercatelli L, Mirabile A, Mungai F, Miele V, Olmastroni M, Pagano P, Paiar F, Panichi G, Pascali Ma, Pasquinelli F, Shortrede Je, Tumminello L, Volterrani L, Neri E, On Behalf Of The Navigator Consortium Group
NAVIGATOR is an Italian regional project to boost precision medicine in oncology with the aim to make it more predictive, preventive, and personalised by advancing translational research based on quantitative imaging and integrative omics analyses. The project's goal is to develop an open imaging biobank for the collection and preservation of a large amount of standardised imaging multimodal datasets, including computed tomography, magnetic resonance imaging, and positron emission tomography data, together with the corresponding patient-related and omics-related relevant information extracted from regional healthcare services using an adapted privacy-preserving model. The project is based on an open-source imaging biobank and an open-science oriented virtual research environment (VRE). Available integrative omics and multi-imaging data of three use cases (prostate cancer, rectal cancer, and gastric cancer) will be collected. All data confined in NAVIGATOR (i.e. standard and novel imaging biomarkers, non-imaging data, health agency data) will be used to create a digital patient model, to support the reliable prediction of the disease phenotype and risk stratification. The VRE that relies on a well-established infrastructure, called D4Science.org, will further provide a multiset infrastructure for processing the integrative omics data, extracting specific radiomic signatures, and for identification and testing of novel imaging biomarkers through big data analytics and artificial intelligence.Source: EUROPEAN RADIOLOGY EXPERIMENTAL, vol. 6 (issue 53)
DOI: 10.1186/s41747-022-00306-9
Metrics:
Borgheresi R, Barucci A, Colantonio S, Aghakhanyan G, Assante M, Bertelli E, Carlini E, Carpi R, Caudai C, Cavallero D, Cioni D, Cirillo R, Colcelli V, Dell'Amico A, Di Gangi D, Erba Pa, Faggioni L, Falaschi Z, Gabelloni M, Gini R, Lelii L, Liò P, Lorito A, Lucarini S, Manghi P, Mangiacrapa F, Marzi C, Mazzei Ma, Mercatelli L, Mirabile A, Mungai F, Miele V, Olmastroni M, Pagano P, Paiar F, Panichi G, Pascali Ma, Pasquinelli F, Shortrede Je, Tumminello L, Volterrani L, Neri E, On Behalf Of The Navigator Consortium Group
NAVIGATOR is an Italian regional project to boost precision medicine in oncology with the aim to make it more predictive, preventive, and personalised by advancing translational research based on quantitative imaging and integrative omics analyses. The project's goal is to develop an open imaging biobank for the collection and preservation of a large amount of standardised imaging multimodal datasets, including computed tomography, magnetic resonance imaging, and positron emission tomography data, together with the corresponding patient-related and omics-related relevant information extracted from regional healthcare services using an adapted privacy-preserving model. The project is based on an open-source imaging biobank and an open-science oriented virtual research environment (VRE). Available integrative omics and multi-imaging data of three use cases (prostate cancer, rectal cancer, and gastric cancer) will be collected. All data confined in NAVIGATOR (i.e. standard and novel imaging biomarkers, non-imaging data, health agency data) will be used to create a digital patient model, to support the reliable prediction of the disease phenotype and risk stratification. The VRE that relies on a well-established infrastructure, called D4Science.org, will further provide a multiset infrastructure for processing the integrative omics data, extracting specific radiomic signatures, and for identification and testing of novel imaging biomarkers through big data analytics and artificial intelligence.Source: EUROPEAN RADIOLOGY EXPERIMENTAL, vol. 6 (issue 53)
DOI: 10.1186/s41747-022-00306-9
Metrics:
See at:
eurradiolexp.springeropen.com | CNR IRIS | ISTI Repository | CNR IRIS
2022
Other
Open Access
Blue-Cloud D4.6 - Blue Cloud VRE Operation Report (Release 2)
M Assante, L Candela, P Pagano, R Cirillo, A Dell'Amico, L Frosini, L Lelii, F Mangiacrapa, G Panichi, F Sinibaldi
The Blue-Cloud project developed a cyber platform bringing together and providing access to multidisciplinary data from observations and models, analytical tools, and computing facilities essential to support research to better understand and manage the many aspects of ocean sustainability. The Blue-Cloud platform architecture consists of two major families of components: (a) the Blue Cloud Data Discovery and Access service to serve federated discovery and access to 'blue data' infrastructures, and (b) the Blue Cloud Virtual Research Environment (VRE) to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This Deliverable D4.6 "Blue Cloud VRE Operation (Release 2)" is the revised and updated version of the D4.1 "Blue Cloud VRE Operation (Release 1)" [10]. It reports on the Blue-Cloud Virtual Research Environment (VRE) by complementing the architecture and infrastructure described in [9], where the constituents have been discussed. Specifically, this deliverable focuses on how the components have been exploited and operated to support the development of the Blue-Cloud gateway https://blue-cloud.d4science.org, its underlying infrastructure, and the VLabs. 9 Blue-Cloud VLabs were created and operated in the first period, while an additional 5 Blue-Cloud VLabs were created and operated in the second reporting period, from M17 (February 2021) to M35 (September 2022), bringing the total on 14 operational VLabs. Two VLabs of the second reporting period are specifically conceived to support the developments of the Blue-Cloud Demonstrators: (i) The Plankton Genomics VLab has been developed in the context of the Demonstrator #2, and (ii) The Marine Environmental Indicators Dev VLab has been developed in the context of the Demonstrator #3 - Marine Environmental Indicators. In order to support the Blue-Cloud Hackathon1 event held in February 2022 the (iii) Blue-Cloud Hackathon VLab has been developed. Finally, in the framework of the Blue-Cloud synergies programme two additional VLabs were developed as pilots to support the work of (iv) the JERICO-CORE multi-platform research infrastructure dedicated to a holistic appraisal of coastal marine system changes, and (v) the JONAS initiative, addressing the issue of underwater noise in the Atlantic Seas. These working environments are serving more than 1,300 users in total spread across more than 20 countries. Up to mid of September 2022, a total of more than 25,700 working sessions have been executed, with an average of 1,286 working sessions per month since the start of the Blue-Cloud project in October 2019. A total of more than 2,230 analytics sessions have been executed by the users of the VLabs, with an average of 55 working sessions per month. From M17 (February 2021) to M35 (September 2022), a total of 212 tickets have been created and managed in the Blue-Cloud Project Issue Trackers (85% have been closed). Moreover, 34 tickets related to Blue-Cloud have been created in the D4Science overall context (88% have been closed).Project(s): Blue Cloud
M Assante, L Candela, P Pagano, R Cirillo, A Dell'Amico, L Frosini, L Lelii, F Mangiacrapa, G Panichi, F Sinibaldi
The Blue-Cloud project developed a cyber platform bringing together and providing access to multidisciplinary data from observations and models, analytical tools, and computing facilities essential to support research to better understand and manage the many aspects of ocean sustainability. The Blue-Cloud platform architecture consists of two major families of components: (a) the Blue Cloud Data Discovery and Access service to serve federated discovery and access to 'blue data' infrastructures, and (b) the Blue Cloud Virtual Research Environment (VRE) to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This Deliverable D4.6 "Blue Cloud VRE Operation (Release 2)" is the revised and updated version of the D4.1 "Blue Cloud VRE Operation (Release 1)" [10]. It reports on the Blue-Cloud Virtual Research Environment (VRE) by complementing the architecture and infrastructure described in [9], where the constituents have been discussed. Specifically, this deliverable focuses on how the components have been exploited and operated to support the development of the Blue-Cloud gateway https://blue-cloud.d4science.org, its underlying infrastructure, and the VLabs. 9 Blue-Cloud VLabs were created and operated in the first period, while an additional 5 Blue-Cloud VLabs were created and operated in the second reporting period, from M17 (February 2021) to M35 (September 2022), bringing the total on 14 operational VLabs. Two VLabs of the second reporting period are specifically conceived to support the developments of the Blue-Cloud Demonstrators: (i) The Plankton Genomics VLab has been developed in the context of the Demonstrator #2, and (ii) The Marine Environmental Indicators Dev VLab has been developed in the context of the Demonstrator #3 - Marine Environmental Indicators. In order to support the Blue-Cloud Hackathon1 event held in February 2022 the (iii) Blue-Cloud Hackathon VLab has been developed. Finally, in the framework of the Blue-Cloud synergies programme two additional VLabs were developed as pilots to support the work of (iv) the JERICO-CORE multi-platform research infrastructure dedicated to a holistic appraisal of coastal marine system changes, and (v) the JONAS initiative, addressing the issue of underwater noise in the Atlantic Seas. These working environments are serving more than 1,300 users in total spread across more than 20 countries. Up to mid of September 2022, a total of more than 25,700 working sessions have been executed, with an average of 1,286 working sessions per month since the start of the Blue-Cloud project in October 2019. A total of more than 2,230 analytics sessions have been executed by the users of the VLabs, with an average of 55 working sessions per month. From M17 (February 2021) to M35 (September 2022), a total of 212 tickets have been created and managed in the Blue-Cloud Project Issue Trackers (85% have been closed). Moreover, 34 tickets related to Blue-Cloud have been created in the D4Science overall context (88% have been closed).Project(s): Blue Cloud
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2022
Other
Open Access
ARIADNEplus D13.4 - VREs Operation Final Activity Report
Assante M, Cirillo R, Dell'Amico A, Pagano P, Candela L, Frosini L, Lelii L, Mangiacrapa F, Panichi G, Piccioli T, Sinibaldi F
Virtual Research Environments (VREs) are "systems" specifically conceived to provide their users with a web-based set of facilities (including services, data and computational facilities) to accomplish a set of tasks by dynamically relying on the underlying infrastructure. VREs are among the key products developed and delivered by the ARIADNEplus project to support the target communities and application scenarios in archaeology. The development of VREs is based on three main activities: (i) the development of software artifacts that realise a set of functions (including those needed for accessing certain datasets), (ii) the deployment of these artifacts in an operational infrastructure following the release procedures and tools presented in the deliverable D13.1 "Software Release Procedures and Tools JRA2", and (iii) the final deployment and operation of well-defined Virtual Research Environments by exploiting the facilities offered by the underlying D4Science infrastructure and its services [1]. This deliverable D13.4 - "VREs Operation Final Activity Report'' is the updated version of D13.2 - "VREs Operation Mid-term Activity Report ''. D13.4 documents the last of the above- mentioned three activities - i.e. the exploitation of the services and technologies offered by the underlying infrastructure to serve the needs of defined scenarios - as implemented in the second period, from January 2021 to November 2022 - of the ARIADNEplus project. Specifically, it focuses on how the components have been exploited and operated to support the development of the ARIADNEplus VRE gateway https://ariadne.d4science.org, its underlying infrastructure, and the VREs from M25 (January 2021) to M47 (November 2022). These activities have been carried out within Work Package 13. Specifically in Task 13.1 Infrastructure Operation (JRA2.1) and Task 13.3 VREs Operation (JRA2.3). In addition to the 5 VREs created and operated in the first period, 3 more VREs were created and operated in the second reporting period, for a total of 8 VREs. One VRE of the second reporting period, namely ARIADNEplus Lab (cf. Section 4.6), was created in July 2021 as the virtual laboratory to support developers, researchers, data managers, and data analysts belonging to the archaeological community worldwide. The "Geoportale Nazionale per l'Archeologia (GNA)" VRE (cf. Section 4.7) was created in January 2022, as the evolution of the existing Geoportal Prototype VRE (cf. Section 4.4), which was developed for the integration, validation, harmonization, visualization, and access of archaeological georeferenced datasets collected in Italy. Finally, the Esquiline VRE (cf. Section 4.8) was created in October 2022 for the integration and display of data originating from 19th century excavations and historical cartography in a spatio-temporal database, allowing the reconstruction of the transformation of an urban landscape through the centuries. As of November 2022, the VREs are serving the needs of more than 400 users in total spread across 21 countries and more than 10.000 user sessions. This required to deal with approximately 100 tickets (59 requests for support, 9 requests for incidents and bugs, 9 requests for Virtual Machine or Container creations).Project(s): ARIADNEplus
Assante M, Cirillo R, Dell'Amico A, Pagano P, Candela L, Frosini L, Lelii L, Mangiacrapa F, Panichi G, Piccioli T, Sinibaldi F
Virtual Research Environments (VREs) are "systems" specifically conceived to provide their users with a web-based set of facilities (including services, data and computational facilities) to accomplish a set of tasks by dynamically relying on the underlying infrastructure. VREs are among the key products developed and delivered by the ARIADNEplus project to support the target communities and application scenarios in archaeology. The development of VREs is based on three main activities: (i) the development of software artifacts that realise a set of functions (including those needed for accessing certain datasets), (ii) the deployment of these artifacts in an operational infrastructure following the release procedures and tools presented in the deliverable D13.1 "Software Release Procedures and Tools JRA2", and (iii) the final deployment and operation of well-defined Virtual Research Environments by exploiting the facilities offered by the underlying D4Science infrastructure and its services [1]. This deliverable D13.4 - "VREs Operation Final Activity Report'' is the updated version of D13.2 - "VREs Operation Mid-term Activity Report ''. D13.4 documents the last of the above- mentioned three activities - i.e. the exploitation of the services and technologies offered by the underlying infrastructure to serve the needs of defined scenarios - as implemented in the second period, from January 2021 to November 2022 - of the ARIADNEplus project. Specifically, it focuses on how the components have been exploited and operated to support the development of the ARIADNEplus VRE gateway https://ariadne.d4science.org, its underlying infrastructure, and the VREs from M25 (January 2021) to M47 (November 2022). These activities have been carried out within Work Package 13. Specifically in Task 13.1 Infrastructure Operation (JRA2.1) and Task 13.3 VREs Operation (JRA2.3). In addition to the 5 VREs created and operated in the first period, 3 more VREs were created and operated in the second reporting period, for a total of 8 VREs. One VRE of the second reporting period, namely ARIADNEplus Lab (cf. Section 4.6), was created in July 2021 as the virtual laboratory to support developers, researchers, data managers, and data analysts belonging to the archaeological community worldwide. The "Geoportale Nazionale per l'Archeologia (GNA)" VRE (cf. Section 4.7) was created in January 2022, as the evolution of the existing Geoportal Prototype VRE (cf. Section 4.4), which was developed for the integration, validation, harmonization, visualization, and access of archaeological georeferenced datasets collected in Italy. Finally, the Esquiline VRE (cf. Section 4.8) was created in October 2022 for the integration and display of data originating from 19th century excavations and historical cartography in a spatio-temporal database, allowing the reconstruction of the transformation of an urban landscape through the centuries. As of November 2022, the VREs are serving the needs of more than 400 users in total spread across 21 countries and more than 10.000 user sessions. This required to deal with approximately 100 tickets (59 requests for support, 9 requests for incidents and bugs, 9 requests for Virtual Machine or Container creations).Project(s): ARIADNEplus
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2022
Other
Open Access
ARIADNEplus D13.3 - Software release final activity report
Assante M, Cirillo R, Frosini L, Millet P, Pagano P, Candela L, Dell'Amico A, Lelii L, Mangiacrapa F, Panichi G
This deliverable D13.3 - "Software Release Final Activity Report - JRA2" documents the software packages produced by the project to implement the functionalities of the ARIADNEplus infrastructure, accessible from https://ariadne.d4science.org. These open- source software releases followed the procedures described in D13.1 Software Release Procedures and Tools - JRA2 governing the release of software, methods, and tools for the ARIADNEplus infrastructure. D13.3 reports on (i) the ARIADNE VRE software releases, where a total of 29 different release cycles were performed during the project period. Each release contained EUPL licensed software, whose source is accessible on the Code Versioning System (CVS) platform publicly available online at https://code-repo.d4science.org/gCubeCI/gCubeReleases, and reports on (ii) the ARIADNE Portal software releases whose source is accessible on the Code Versioning System (CVS) platform publicly available online https://github.com/ARIADNE- Infrastructure/portal. These activities have been carried out in the context of Task 13.4 Software integration and release (JRA2.4) as part of Work Package 13 (WP13). This task managed the process of software maintenance, enhancement, and provisioning in JRA work packages. Thus, it i) defines the release and provisioning procedures; ii) establishes the release plan; iii) coordinates the release process; iv) operates the tools required to support the release and provisioning activities; v) validates the software documentation; vi) takes care of the distribution of the software and its provisioning. This task benefits from the practices established and experience gained within the D4Science infrastructure.Project(s): ARIADNEplus
Assante M, Cirillo R, Frosini L, Millet P, Pagano P, Candela L, Dell'Amico A, Lelii L, Mangiacrapa F, Panichi G
This deliverable D13.3 - "Software Release Final Activity Report - JRA2" documents the software packages produced by the project to implement the functionalities of the ARIADNEplus infrastructure, accessible from https://ariadne.d4science.org. These open- source software releases followed the procedures described in D13.1 Software Release Procedures and Tools - JRA2 governing the release of software, methods, and tools for the ARIADNEplus infrastructure. D13.3 reports on (i) the ARIADNE VRE software releases, where a total of 29 different release cycles were performed during the project period. Each release contained EUPL licensed software, whose source is accessible on the Code Versioning System (CVS) platform publicly available online at https://code-repo.d4science.org/gCubeCI/gCubeReleases, and reports on (ii) the ARIADNE Portal software releases whose source is accessible on the Code Versioning System (CVS) platform publicly available online https://github.com/ARIADNE- Infrastructure/portal. These activities have been carried out in the context of Task 13.4 Software integration and release (JRA2.4) as part of Work Package 13 (WP13). This task managed the process of software maintenance, enhancement, and provisioning in JRA work packages. Thus, it i) defines the release and provisioning procedures; ii) establishes the release plan; iii) coordinates the release process; iv) operates the tools required to support the release and provisioning activities; v) validates the software documentation; vi) takes care of the distribution of the software and its provisioning. This task benefits from the practices established and experience gained within the D4Science infrastructure.Project(s): ARIADNEplus
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2022
Software
Metadata Only Access
dnet-dedup framework
Artini M., Atzori C., Bardi A., Baglioni M., De Bonis M., Dell'Amico A., La Bruzzo S. F., Mannocci A., Manghi P.
The GDup Software enables an integrated, scalable, general-purpose system for entity deduplication over big information graphs. GDup supports practitioners with the functionalities needed to realize a fully-fledged entity deduplication workflow over a generic input graph, including Ground Truth support, end-user feedback, and strategies for identifying and merging duplicates to obtain an output disambiguated graph. GDup is today one of the core components of the OpenAIRE infrastructure production system, monitoring Open Science trends on behalf of the European Commission.Project(s): OpenAIRE-Advance, OpenAIRE Nexus
Artini M., Atzori C., Bardi A., Baglioni M., De Bonis M., Dell'Amico A., La Bruzzo S. F., Mannocci A., Manghi P.
The GDup Software enables an integrated, scalable, general-purpose system for entity deduplication over big information graphs. GDup supports practitioners with the functionalities needed to realize a fully-fledged entity deduplication workflow over a generic input graph, including Ground Truth support, end-user feedback, and strategies for identifying and merging duplicates to obtain an output disambiguated graph. GDup is today one of the core components of the OpenAIRE infrastructure production system, monitoring Open Science trends on behalf of the European Commission.Project(s): OpenAIRE-Advance
, OpenAIRE Nexus
See at:
github.com | CNR IRIS
2022
Other
Open Access
OpenAIRE Research Graph: aggregation workflow
La Bruzzo Sf, Artini M, Atzori C, Bardi A, Baglioni M, De Bonis M, Dell'Amico A, Mannocci A, Manghi P, Pavone G
The OpenAIRE Graph (formerly the OpenAIRE Research Graph) is one of the largest open scholarly record collections worldwide. It is key in fostering Open Science and establishing its practices in daily research activities. Conceived as a public and transparent good, populated out of data sources trusted by scientists, the Graph aims at bringing discovery, monitoring, and assessment of science back into the hands of the scientific community. OpenAIRE collects metadata records from more than 70K scholarly communication sources worldwide, including Open Access institutional repositories, data archives, and journals. All the metadata records (i.e., descriptions of research products) are put together in a data lake with records from Crossref, Unpaywall, ORCID, ROR, and information about projects provided by national and international funders. This technical Report describes the main Aggregation Workflow to orchestrate the data aggregation and the implemented mapping from some of the main datasources into the OpenAIRE research graph data model.DOI: 10.32079/isti-tr-2022/033
Project(s): OpenAIRE-Advance, OpenAIRE Nexus
Metrics:
La Bruzzo Sf, Artini M, Atzori C, Bardi A, Baglioni M, De Bonis M, Dell'Amico A, Mannocci A, Manghi P, Pavone G
The OpenAIRE Graph (formerly the OpenAIRE Research Graph) is one of the largest open scholarly record collections worldwide. It is key in fostering Open Science and establishing its practices in daily research activities. Conceived as a public and transparent good, populated out of data sources trusted by scientists, the Graph aims at bringing discovery, monitoring, and assessment of science back into the hands of the scientific community. OpenAIRE collects metadata records from more than 70K scholarly communication sources worldwide, including Open Access institutional repositories, data archives, and journals. All the metadata records (i.e., descriptions of research products) are put together in a data lake with records from Crossref, Unpaywall, ORCID, ROR, and information about projects provided by national and international funders. This technical Report describes the main Aggregation Workflow to orchestrate the data aggregation and the implemented mapping from some of the main datasources into the OpenAIRE research graph data model.DOI: 10.32079/isti-tr-2022/033
Project(s): OpenAIRE-Advance
, OpenAIRE Nexus Metrics:
See at:
CNR IRIS | ISTI Repository | CNR IRIS
2022
Other
Restricted
OPEN-ASFA Final Report
Assante M, Dell'Amico A, Pagano P, Piccioli T
This document describes the services exploited by the Open-ASFA Virtual Research Environment (OPEN-ASFA VRE) at final term. It reports metrics of usage, the status of the activities, including service upgrades, and a summary of the issues solved or to be solved, from November 1st 2021 to April 30th 2022.
Assante M, Dell'Amico A, Pagano P, Piccioli T
This document describes the services exploited by the Open-ASFA Virtual Research Environment (OPEN-ASFA VRE) at final term. It reports metrics of usage, the status of the activities, including service upgrades, and a summary of the issues solved or to be solved, from November 1st 2021 to April 30th 2022.