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) (2022). doi:10.1002/cpe.6925
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) (2022). doi:10.1002/cpe.6925
DOI: 10.1002/cpe.6925
Project(s): AGINFRA PLUS
, Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus Metrics:
See at:
ISTI Repository 
| onlinelibrary.wiley.com 
| CNR ExploRA
2022
Report
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.Source: ISTI Annual report, 2022
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.Source: ISTI Annual report, 2022
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:
ISTI Repository | CNR ExploRA
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 P. A., Faggioni L., Falaschi Z., Gabelloni M., Gini R., Lelii L., Liò P., Lorito A., Lucarini S., Manghi P., Mangiacrapa F., Marzi C., Mazzei M. A., Mercatelli L., Mirabile A., Mungai F., Miele V., Olmastroni M., Pagano P., Paiar F., Panichi G., Pascali M. A., Pasquinelli F., Shortrede J. E., 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 Online 6 (2022). doi:10.1186/s41747-022-00306-9
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 P. A., Faggioni L., Falaschi Z., Gabelloni M., Gini R., Lelii L., Liò P., Lorito A., Lucarini S., Manghi P., Mangiacrapa F., Marzi C., Mazzei M. A., Mercatelli L., Mirabile A., Mungai F., Miele V., Olmastroni M., Pagano P., Paiar F., Panichi G., Pascali M. A., Pasquinelli F., Shortrede J. E., 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 Online 6 (2022). doi:10.1186/s41747-022-00306-9
DOI: 10.1186/s41747-022-00306-9
Metrics:
See at:
eurradiolexp.springeropen.com | ISTI Repository | CNR ExploRA
2022
Report
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).Source: ISTI Project report, Blue-Cloud, D4.6, 2022
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).Source: ISTI Project report, Blue-Cloud, D4.6, 2022
Project(s): Blue Cloud
See at:
ISTI Repository | CNR ExploRA
2022
Report
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).Source: ISTI Project report, ARIADNEplus, D13.4, 2022
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).Source: ISTI Project report, ARIADNEplus, D13.4, 2022
Project(s): ARIADNEplus
See at:
ISTI Repository | CNR ExploRA
2022
Report
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.Source: ISTI Project report, ARIADNEplus, D13.3, 2022
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.Source: ISTI Project report, ARIADNEplus, D13.3, 2022
Project(s): ARIADNEplus
See at:
ISTI Repository | CNR ExploRA
2022
Report
Closed Access
D4Science Activity Report 2022
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Dell'Amico A., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Piccioli T., Sinibaldi F., Zoppi F.
D4Science is an IT infrastructure specifically conceived to support the development and operation of Virtual Research Environments by the as-a-Service provisioning mode. This report documents the activities performed in 2022 to develop this infrastructure and support several projects and exploitations.Source: ISTI Technical Report, ISTI-2022-TR/037, 2022
DOI: 10.32079/isti-tr-2022/037
Project(s): ARIADNEplus, Blue Cloud , EOSC-Pillar , DESIRA , SoBigData-PlusPlus
Metrics:
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Dell'Amico A., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Piccioli T., Sinibaldi F., Zoppi F.
D4Science is an IT infrastructure specifically conceived to support the development and operation of Virtual Research Environments by the as-a-Service provisioning mode. This report documents the activities performed in 2022 to develop this infrastructure and support several projects and exploitations.Source: ISTI Technical Report, ISTI-2022-TR/037, 2022
DOI: 10.32079/isti-tr-2022/037
Project(s): ARIADNEplus
, Blue Cloud , EOSC-Pillar , DESIRA , SoBigData-PlusPlus Metrics:
See at:
CNR ExploRA
2022
Report
Closed Access
InfraScience research activity report 2022
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., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Ottonello E., Pagano P., Panichi G., Pavone G., Piccioli T., Sinibaldi F., Straccia U., Zoppi F.
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 2022 to highlight the major results. In particular, the InfraScience group confronted with 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 2022 InfraScience members contributed to the publishing of several 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.Source: ISTI Annual reports, 2022
Project(s): ARIADNEplus, Blue Cloud , EOSC-Pillar , DESIRA , EOSC Future , RISIS 2 , TAILOR , SoBigData-PlusPlus
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., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Ottonello E., Pagano P., Panichi G., Pavone G., Piccioli T., Sinibaldi F., Straccia U., Zoppi F.
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 2022 to highlight the major results. In particular, the InfraScience group confronted with 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 2022 InfraScience members contributed to the publishing of several 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.Source: ISTI Annual reports, 2022
Project(s): ARIADNEplus
, Blue Cloud , EOSC-Pillar , DESIRA , EOSC Future , RISIS 2 , TAILOR , SoBigData-PlusPlus
See at:
CNR ExploRA
2021
Report
Open Access
ARIADNEPlus - VREs operation mid-term activity report
Assante M., Cirillo R., Dell'Amico A., Pagano P., Candela L., Frosini L., Lelii L., Mangiacrapa F., Panichi G., Sinibaldi F.
This deliverable D13.2 - "VREs Operation Mid-term Activity Report" describes the activities carried out during the first 24 months of the ARIADNEplus project within Work Package 13. Specifically, in Task 13.1 Infrastructure Operation (JRA2.1) and Task 13.3 VREs Operation (JRA2.3). It reports the procedures governing the operation of the VREs as well as the status of the aggregated resources at mid-term in the ARIADNEplus infrastructure.Source: Project report, ARIADNEplus, D13.2, 2021
Project(s): ARIADNEplus
Assante M., Cirillo R., Dell'Amico A., Pagano P., Candela L., Frosini L., Lelii L., Mangiacrapa F., Panichi G., Sinibaldi F.
This deliverable D13.2 - "VREs Operation Mid-term Activity Report" describes the activities carried out during the first 24 months of the ARIADNEplus project within Work Package 13. Specifically, in Task 13.1 Infrastructure Operation (JRA2.1) and Task 13.3 VREs Operation (JRA2.3). It reports the procedures governing the operation of the VREs as well as the status of the aggregated resources at mid-term in the ARIADNEplus infrastructure.Source: Project report, ARIADNEplus, D13.2, 2021
Project(s): ARIADNEplus
See at:
ISTI Repository | CNR ExploRA
2021
Conference article
Open Access
Realising a science gateway for the Agri-food: the AGINFRAplus experience
Assante M., Boizet A., Candela L., Castelli D., Cirillo R., Coro G., Fernandez E., Filter M., Frosini L., Kakaletris G., Katsivelis P., Knapen R., Lelii L., Lokers R., Mangiacrapa F., Pagano P., Panichi G., Penev L., Sinibaldi F., Zervas P.
The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing and analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the "assets" to be exploited when performing research tasks, e.g. data of interest are heterogeneous and scattered across several repositories, the tools modellers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the "whole story" with datasets, processes, workflows. This paper presents the AGINFRA PLUS endeavour to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the "assets" of interest and promote collaboration.Source: 11th International Workshop on Science Gateways, Ljubljana, Slovenia, 12-14/06/2019
Project(s): AGINFRA PLUS
Assante M., Boizet A., Candela L., Castelli D., Cirillo R., Coro G., Fernandez E., Filter M., Frosini L., Kakaletris G., Katsivelis P., Knapen R., Lelii L., Lokers R., Mangiacrapa F., Pagano P., Panichi G., Penev L., Sinibaldi F., Zervas P.
The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing and analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the "assets" to be exploited when performing research tasks, e.g. data of interest are heterogeneous and scattered across several repositories, the tools modellers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the "whole story" with datasets, processes, workflows. This paper presents the AGINFRA PLUS endeavour to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the "assets" of interest and promote collaboration.Source: 11th International Workshop on Science Gateways, Ljubljana, Slovenia, 12-14/06/2019
Project(s): AGINFRA PLUS
See at:
ceur-ws.org | ISTI Repository | CNR ExploRA
2021
Report
Open Access
InfraScience Research Activity Report 2020
Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Candela L., Casini G., Castelli D., Cirillo R., Coro G., Debole F., Dell'Amico A., Frosini L., La Bruzzo S., Lazzeri E., Lelii L., Manghi P., Mangiacrapa F., Mannocci A., Pagano P., Panichi 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 2020 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, e\-Sci\-ence, 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, \ie D4Science and OpenAIRE. During 2020 InfraScience members contributed to the publishing of 30 papers, to the research and development activities of 12 research projects (11 funded by EU), to the organization of conferences and training events, to several working groups and task forces.Source: ISTI Annual Report, ISTI-2021-AR/002, pp.1–20, 2021
DOI: 10.32079/isti-ar-2021/002
Project(s): ARIADNEplus, Blue Cloud , PerformFISH , EOSC-Pillar , DESIRA , EOSCsecretariat.eu , RISIS 2 , TAILOR , I-GENE , MOVING , OpenAIRE-Advance , SoBigData-PlusPlus
Metrics:
Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Candela L., Casini G., Castelli D., Cirillo R., Coro G., Debole F., Dell'Amico A., Frosini L., La Bruzzo S., Lazzeri E., Lelii L., Manghi P., Mangiacrapa F., Mannocci A., Pagano P., Panichi 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 2020 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, e\-Sci\-ence, 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, \ie D4Science and OpenAIRE. During 2020 InfraScience members contributed to the publishing of 30 papers, to the research and development activities of 12 research projects (11 funded by EU), to the organization of conferences and training events, to several working groups and task forces.Source: ISTI Annual Report, ISTI-2021-AR/002, pp.1–20, 2021
DOI: 10.32079/isti-ar-2021/002
Project(s): ARIADNEplus
, Blue Cloud , PerformFISH , EOSC-Pillar , DESIRA , EOSCsecretariat.eu , RISIS 2 , TAILOR , I-GENE , MOVING , OpenAIRE-Advance , SoBigData-PlusPlus Metrics:
See at:
ISTI Repository | CNR ExploRA
2021
Report
Open Access
Blue Cloud - D4.4: Blue Cloud VRE Common Facilities (Release 2)
Assante M., Candela L., Pagano P., Cirillo R., Dell'Amico A., Frosini L., Lelii L., Lettere M., Mangiacrapa F., Panichi G., Sinibaldi F.
The Blue-Cloud project is piloting 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 understand better and manage the many aspects of ocean sustainability. This goal is realised by developing, deploying and operating the Blue-Cloud platform whose architecture consists of two major families of components: (a) the Blue Cloud Data Discovery and Access System to serve federated discovery and access to 'blue data' infrastructures; and (b) the Blue Cloud Virtual Research Environment (VRE) component to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This Deliverable D4.4 "Blue Cloud VRE Common Facilities (Release 2)" is the revised version of the D4.2 "Blue Cloud VRE Common Facilities (Release 1)". This revised version of the document covers the second period of the project, from M13 up to M27, including the up-to-date information of the services reported on D4.2 and the new services that have been developed and added to the VRE common facilities in the reporting period to serve the needs of the Blue Cloud community. The major changes and new services this deliverable introduces are: an Orchestrator (cf. Sec. 3.3), i.e. a software that allows for a declarative, technology agnostic definition of workflows to coordinate the execution of tasks across diverse services and systems; enhancements to the Workspace service to support tailored storage persistence and satisfy different application scenarios (cf. Sec. 4.1); enhancements in the Publishing Framework (cf. Sec. 6), namely the catalogue extension to deposit catalogue items to Zenodo and the facility to publish geospatial data from the workspace; the facility to interface with the Data Discovery & Access System (cf. Sec. 7.1) to transfer datasets of interest into the workspace for future uses; the notebook to facilitate the exploitation of the WEkEO Harmonised Data Access (HDA) API (cf. Sec. 7.2). This deliverable also updates the Identity and Access Management (cf. Sec. 3.1) and the Analytics Framework (cf. Sec. 5.1 and Sec 5.2) with minor changes reflecting the activities performed in the reporting period. A description of all the services previously documented in D4.2, not modified in the period, is preserved for this document to be self-contained and provide the reader with an overall description of the whole VRE Common Facilities offering. A total of 15 services and components are described in this deliverable by reporting their design principles, architecture and main features. These services and components contribute functionalities to the Blue Cloud VRE Enabling Framework (Identity and Access Management, VRE Management, Orchestrator), Collaborative framework (Workspace and Social Networking), Analytics Framework (Software and Algorithm Importer, Smart Executor), Publishing Framework (Catalogue Service) and improved support for RStudio, JupyterHub, ShinyProxy, and Docker Applications. Additionally, two new VRE services, aiming at bridging two VRE external systems such as the the WEkEO1 catalogue from Copernicus and the Data Discovery and Access from Blue-Cloud with the VRE tools are described. Services and components discussed in this deliverable have contributed to 14 gCube releases, from gCube 4.26 (November 2020) to gCube 5.6.0 (November 2021). They have been used to develop and operate the Virtual Laboratories of the Blue Cloud gateway https://blue-cloud.d4science.org and its underlying infrastructure. At the time of this deliverable the Blue-Cloud gateway and its services are serving more than 730 users with a total of 19000+ working sessions.Source: ISTI Project report, Blue Cloud, D4.4, 2021
Project(s): Blue Cloud
Assante M., Candela L., Pagano P., Cirillo R., Dell'Amico A., Frosini L., Lelii L., Lettere M., Mangiacrapa F., Panichi G., Sinibaldi F.
The Blue-Cloud project is piloting 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 understand better and manage the many aspects of ocean sustainability. This goal is realised by developing, deploying and operating the Blue-Cloud platform whose architecture consists of two major families of components: (a) the Blue Cloud Data Discovery and Access System to serve federated discovery and access to 'blue data' infrastructures; and (b) the Blue Cloud Virtual Research Environment (VRE) component to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This Deliverable D4.4 "Blue Cloud VRE Common Facilities (Release 2)" is the revised version of the D4.2 "Blue Cloud VRE Common Facilities (Release 1)". This revised version of the document covers the second period of the project, from M13 up to M27, including the up-to-date information of the services reported on D4.2 and the new services that have been developed and added to the VRE common facilities in the reporting period to serve the needs of the Blue Cloud community. The major changes and new services this deliverable introduces are: an Orchestrator (cf. Sec. 3.3), i.e. a software that allows for a declarative, technology agnostic definition of workflows to coordinate the execution of tasks across diverse services and systems; enhancements to the Workspace service to support tailored storage persistence and satisfy different application scenarios (cf. Sec. 4.1); enhancements in the Publishing Framework (cf. Sec. 6), namely the catalogue extension to deposit catalogue items to Zenodo and the facility to publish geospatial data from the workspace; the facility to interface with the Data Discovery & Access System (cf. Sec. 7.1) to transfer datasets of interest into the workspace for future uses; the notebook to facilitate the exploitation of the WEkEO Harmonised Data Access (HDA) API (cf. Sec. 7.2). This deliverable also updates the Identity and Access Management (cf. Sec. 3.1) and the Analytics Framework (cf. Sec. 5.1 and Sec 5.2) with minor changes reflecting the activities performed in the reporting period. A description of all the services previously documented in D4.2, not modified in the period, is preserved for this document to be self-contained and provide the reader with an overall description of the whole VRE Common Facilities offering. A total of 15 services and components are described in this deliverable by reporting their design principles, architecture and main features. These services and components contribute functionalities to the Blue Cloud VRE Enabling Framework (Identity and Access Management, VRE Management, Orchestrator), Collaborative framework (Workspace and Social Networking), Analytics Framework (Software and Algorithm Importer, Smart Executor), Publishing Framework (Catalogue Service) and improved support for RStudio, JupyterHub, ShinyProxy, and Docker Applications. Additionally, two new VRE services, aiming at bridging two VRE external systems such as the the WEkEO1 catalogue from Copernicus and the Data Discovery and Access from Blue-Cloud with the VRE tools are described. Services and components discussed in this deliverable have contributed to 14 gCube releases, from gCube 4.26 (November 2020) to gCube 5.6.0 (November 2021). They have been used to develop and operate the Virtual Laboratories of the Blue Cloud gateway https://blue-cloud.d4science.org and its underlying infrastructure. At the time of this deliverable the Blue-Cloud gateway and its services are serving more than 730 users with a total of 19000+ working sessions.Source: ISTI Project report, Blue Cloud, D4.4, 2021
Project(s): Blue Cloud
See at:
ISTI Repository | CNR ExploRA
2021
Report
Open Access
DESIRA - D5.2: Virtual Research Environment Operation Report years 1-2
Assante M., Candela L., Cirillo R., Dell'Amico A., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Sinibaldi F.
This deliverable D5.2 "Virtual Research Environment Operation Report years 1-2" describes the activities carried out during the first 24 months of 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 mid-term 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 from June 2019 to May 2021. The DESIRA Infrastructure Gateway actually offers end-user access to 14 VREs. As of June 2019, 1 VREs were created and operated. Specifically, the DESIRA Project VRE (cf. Sec 3.1.1) was created before the project kick-off. As of May 2021, these VREs have served the needs of more than 370 users and more than 7.000 user sessions. This required dealing with 177 tickets (103 related to the project management, 28 requests for support and enhancements, five requests for incidents and bugs, 14 requests for VRE creations).Source: ISTI Project report, DESIRA, D5.2, 2021
Project(s): DESIRA
Assante M., Candela L., Cirillo R., Dell'Amico A., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Sinibaldi F.
This deliverable D5.2 "Virtual Research Environment Operation Report years 1-2" describes the activities carried out during the first 24 months of 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 mid-term 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 from June 2019 to May 2021. The DESIRA Infrastructure Gateway actually offers end-user access to 14 VREs. As of June 2019, 1 VREs were created and operated. Specifically, the DESIRA Project VRE (cf. Sec 3.1.1) was created before the project kick-off. As of May 2021, these VREs have served the needs of more than 370 users and more than 7.000 user sessions. This required dealing with 177 tickets (103 related to the project management, 28 requests for support and enhancements, five requests for incidents and bugs, 14 requests for VRE creations).Source: ISTI Project report, DESIRA, D5.2, 2021
Project(s): DESIRA
See at:
ISTI Repository | CNR ExploRA
2021
Report
Open Access
SoBigData-PlusPlus - D9.1: SoBigData e-Infrastructure Operation Report 1
Assante M., Candela L., Cirilli R., Dell'Amico A., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Sinibaldi F.
This deliverable describes the activities carried out during the first 18 months within Work Package 9 for the SoBigData e-Infrastructure operation activity since its deployment, including a detailed set of usage indicators (i.e. the number of users, accesses 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 ones for the services devoted to Data Analytics. A total of 15 Virtual Research Environments (VREs) have been created and are operational. In particular, the SoBigData gateway 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); 2 Virtual Lab VREs - SoBigDataLab and OpenScienceGraphLab to exploit and experiment tools and solutions; 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-PlusPlus WP9; and 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 June '21, the 15 existing VREs served more than 8,000 users by a total of more than 30,000 working sessions, with an average of 1500 working sessions per month with increasing trend. This required to deal with approximately 40 issue tracker tickets (14 requests for support, 6 requests for incidents and bugs, 9 requests for new features, and 9 requests for Virtual Machine or Container creations).Source: ISTI Project report, SoBigData-PlusPlus, D9.1, 2021
Project(s): SoBigData-PlusPlus
Assante M., Candela L., Cirilli R., Dell'Amico A., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Sinibaldi F.
This deliverable describes the activities carried out during the first 18 months within Work Package 9 for the SoBigData e-Infrastructure operation activity since its deployment, including a detailed set of usage indicators (i.e. the number of users, accesses 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 ones for the services devoted to Data Analytics. A total of 15 Virtual Research Environments (VREs) have been created and are operational. In particular, the SoBigData gateway 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); 2 Virtual Lab VREs - SoBigDataLab and OpenScienceGraphLab to exploit and experiment tools and solutions; 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-PlusPlus WP9; and 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 June '21, the 15 existing VREs served more than 8,000 users by a total of more than 30,000 working sessions, with an average of 1500 working sessions per month with increasing trend. This required to deal with approximately 40 issue tracker tickets (14 requests for support, 6 requests for incidents and bugs, 9 requests for new features, and 9 requests for Virtual Machine or Container creations).Source: ISTI Project report, SoBigData-PlusPlus, D9.1, 2021
Project(s): SoBigData-PlusPlus
See at:
CNR ExploRA
2020
Journal article
Open Access
Realizing virtual research environments for the agri-food community: the AGINFRA PLUS experience
Assante M., Boizet A., Candela L., Castelli D., Cirillo R., Coro G., Fernández E., Filter M., Frosini L., Georgiev T., Kakaletris G., Katsivelis P., Knapen R., Lelii L., Lokers R. M., Mangiacrapa F., Manouselis N., Pagano P., Panichi G., Penev L., Sinibaldi F.
The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing, analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the "assets" to be exploited when performing research tasks, for example, data of interest are heterogeneous and scattered across several repositories, the tools modelers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the "whole story" including datasets, processes, and results. This paper presents the AGINFRA PLUS endeavor to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the "assets" of interest and promote collaboration.Source: Concurrency and computation (Online) 33 (2020). doi:10.1002/cpe.6087
DOI: 10.1002/cpe.6087
Project(s): AGINFRA PLUS
Metrics:
Assante M., Boizet A., Candela L., Castelli D., Cirillo R., Coro G., Fernández E., Filter M., Frosini L., Georgiev T., Kakaletris G., Katsivelis P., Knapen R., Lelii L., Lokers R. M., Mangiacrapa F., Manouselis N., Pagano P., Panichi G., Penev L., Sinibaldi F.
The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing, analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the "assets" to be exploited when performing research tasks, for example, data of interest are heterogeneous and scattered across several repositories, the tools modelers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the "whole story" including datasets, processes, and results. This paper presents the AGINFRA PLUS endeavor to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the "assets" of interest and promote collaboration.Source: Concurrency and computation (Online) 33 (2020). doi:10.1002/cpe.6087
DOI: 10.1002/cpe.6087
Project(s): AGINFRA PLUS
Metrics:
See at:
ISTI Repository | Concurrency and Computation Practice and Experience | Hyper Article en Ligne | onlinelibrary.wiley.com | CNR ExploRA | NARCIS
2020
Report
Open Access
Blue Cloud - D4.2: Blue Cloud VRE Common Facilities (Release 1)
Assante M., Candela L., Pagano P., Dell'Amico A., Coro G., Cirillo R., Frosini L., Lelii L., Lettere M., Mangiacrapa F., Panichi G., Sinibaldi F.
The Blue-Cloud project plans to pilot 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 understand better and manage the many aspects of ocean sustainability. To achieve this goal, Blue-Cloud is developing, deploying, and operating the Blue-Cloud platform whose architecture consists of two families of components: (a) the Blue Cloud Data Discovery and Access service component to serve federated discovery and access to 'blue data' infrastructures; and (b) the Blue Cloud Virtual Research Environment (VRE) component to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This deliverable presents the Blue Cloud Virtual Research Environment constituents by focusing on both new services and revised existing services that have been developed in the reporting period to serve the needs of the Blue Cloud community. In particular, this deliverable describes a total of 11 services and components. These services and components contribute functionalities to the Blue Cloud VRE Enabling Framework (Identity and Access Management, VRE Management), Collaborative framework (Workspace and Social Networking), Analytics Framework (Software and Algorithm Importer, Smart Executor), Publishing Framework (Catalogue Service) and improved support for RStudio, JupyterHub, ShinyProxy, and Docker Applications. The services are described below by reporting their design principles, architectures, and main features. The deliverable also describes the procedures and approaches governing services and components released by highlighting how Gitea (as Git hosting service), Jenkins (as automation server), and Maven (as project management and comprehension tool) are used to guarantee continuous integration processes. Services and components discussed in this deliverable contribute to 11 gCube open-source software system releases (from gCube 4.16 up to gCube 4.25.1) and are in the pipeline for the next ones. They have been used to develop and operate the Virtual Laboratories of the Blue Cloud gateway https://blue-cloud.d4science.org and its underlying infrastructure. At the time of this deliverable (November 2020), the gateway hosts a total of 8 VREs and VLabs, including five specifically conceived to support the co-development of some of the Blue-Cloud demonstrators (namely, the Aquaculture Atlas Generation for Demonstrator #5, the Blue-Cloud Lab for several demonstrators, the GRSF pre for Demonstrator #4, the Marine Environmental Indicators for Demonstrator #3, the Zoo-Phytoplankton EOV for Demonstrator #1). This gateway and its tools serve more than 400 users that (since January 2020) performed a total of more than 5000 working sessions, more than 1700 accesses to the Workspace, and more than 750 analytics tasks. These exploitation and uptake indicators are likely to grow in the coming months thanks to data updates and continued use, further development of existing VLabs, and finally, the creation of new ones.Source: Project Report, Blue Cloud, D4.2, 2020
Project(s): Blue Cloud
Assante M., Candela L., Pagano P., Dell'Amico A., Coro G., Cirillo R., Frosini L., Lelii L., Lettere M., Mangiacrapa F., Panichi G., Sinibaldi F.
The Blue-Cloud project plans to pilot 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 understand better and manage the many aspects of ocean sustainability. To achieve this goal, Blue-Cloud is developing, deploying, and operating the Blue-Cloud platform whose architecture consists of two families of components: (a) the Blue Cloud Data Discovery and Access service component to serve federated discovery and access to 'blue data' infrastructures; and (b) the Blue Cloud Virtual Research Environment (VRE) component to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This deliverable presents the Blue Cloud Virtual Research Environment constituents by focusing on both new services and revised existing services that have been developed in the reporting period to serve the needs of the Blue Cloud community. In particular, this deliverable describes a total of 11 services and components. These services and components contribute functionalities to the Blue Cloud VRE Enabling Framework (Identity and Access Management, VRE Management), Collaborative framework (Workspace and Social Networking), Analytics Framework (Software and Algorithm Importer, Smart Executor), Publishing Framework (Catalogue Service) and improved support for RStudio, JupyterHub, ShinyProxy, and Docker Applications. The services are described below by reporting their design principles, architectures, and main features. The deliverable also describes the procedures and approaches governing services and components released by highlighting how Gitea (as Git hosting service), Jenkins (as automation server), and Maven (as project management and comprehension tool) are used to guarantee continuous integration processes. Services and components discussed in this deliverable contribute to 11 gCube open-source software system releases (from gCube 4.16 up to gCube 4.25.1) and are in the pipeline for the next ones. They have been used to develop and operate the Virtual Laboratories of the Blue Cloud gateway https://blue-cloud.d4science.org and its underlying infrastructure. At the time of this deliverable (November 2020), the gateway hosts a total of 8 VREs and VLabs, including five specifically conceived to support the co-development of some of the Blue-Cloud demonstrators (namely, the Aquaculture Atlas Generation for Demonstrator #5, the Blue-Cloud Lab for several demonstrators, the GRSF pre for Demonstrator #4, the Marine Environmental Indicators for Demonstrator #3, the Zoo-Phytoplankton EOV for Demonstrator #1). This gateway and its tools serve more than 400 users that (since January 2020) performed a total of more than 5000 working sessions, more than 1700 accesses to the Workspace, and more than 750 analytics tasks. These exploitation and uptake indicators are likely to grow in the coming months thanks to data updates and continued use, further development of existing VLabs, and finally, the creation of new ones.Source: Project Report, Blue Cloud, D4.2, 2020
Project(s): Blue Cloud
See at:
ISTI Repository | CNR ExploRA
2019
Report
Open Access
SoBigData - D10.7 - SoBigData e-infrastructure and VRE release
Assante M., Candela L., Cirillo R., Frosini L., Lelii L., Mangiacrapa F., Pagano P.
This deliverable describes the software that has been deployed to serve the needs of the SoBigData community, by delivering the platform and the VREs planned in "D10.4 SoBigData e-Infrastructure release plan 3". In particular, it reports on how such software has been exploited to make available the envisaged components, i.e. the SoBigData portal (and the underlying Virtual Organisation), the SoBigData Catalogue and the SoBigData Virtual Research Environments, together with the list and pointers to the software packages produced by the project and implementing such components, whose operation today constitutes the SoBigData e-infrastructure accessible from http://sobigdata.d4science.org.Source: Project report, SoBigData, Deliverable D10.7, pp.1–28, 2019
Project(s): SoBigData
Assante M., Candela L., Cirillo R., Frosini L., Lelii L., Mangiacrapa F., Pagano P.
This deliverable describes the software that has been deployed to serve the needs of the SoBigData community, by delivering the platform and the VREs planned in "D10.4 SoBigData e-Infrastructure release plan 3". In particular, it reports on how such software has been exploited to make available the envisaged components, i.e. the SoBigData portal (and the underlying Virtual Organisation), the SoBigData Catalogue and the SoBigData Virtual Research Environments, together with the list and pointers to the software packages produced by the project and implementing such components, whose operation today constitutes the SoBigData e-infrastructure accessible from http://sobigdata.d4science.org.Source: Project report, SoBigData, Deliverable D10.7, pp.1–28, 2019
Project(s): SoBigData
See at:
data.d4science.net | ISTI Repository | CNR ExploRA
2019
Journal article
Open Access
The gCube system: delivering virtual research environments as-a-service
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Frosini L., Lelii L., Mangiacrapa F., Marioli V., Pagano P., Panichi G., Perciante C., Sinibaldi F.
Important changes have characterised research and knowledge production in recent decades. These changes are associated with developments in information technologies and infrastructures. The processes characterising research and knowledge production are changing through the digitalization of science, the virtualisation of research communities and networks, the offering of underlying systems and services by infrastructures. This paper gives an overview of gCube, a software system promoting elastic and seamless access to research assets (data, services, computing) across the boundaries of institutions, disciplines and providers to favour collaboration-oriented research tasks. gCube's technology is primarily conceived to enable Hybrid Data Infrastructures facilitating the dynamic definition and operation of Virtual Research Environments. To this end, it offers a comprehensive set of data management commodities on various types of data and a rich array of "mediators" to interface well-established Infrastructures and Information Systems from various domains. Its effectiveness has been proved by operating the D4Science.org infrastructure and serving concrete, multidisciplinary, challenging, and large scale scenarios.Source: Future generation computer systems 95 (2019): 445–453. doi:10.1016/j.future.2018.10.035
DOI: 10.1016/j.future.2018.10.035
DOI: 10.5281/zenodo.3080894
DOI: 10.5281/zenodo.3080895
Project(s): AGINFRA PLUS, BlueBRIDGE , ENVRI PLUS , EOSCpilot
Metrics:
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Frosini L., Lelii L., Mangiacrapa F., Marioli V., Pagano P., Panichi G., Perciante C., Sinibaldi F.
Important changes have characterised research and knowledge production in recent decades. These changes are associated with developments in information technologies and infrastructures. The processes characterising research and knowledge production are changing through the digitalization of science, the virtualisation of research communities and networks, the offering of underlying systems and services by infrastructures. This paper gives an overview of gCube, a software system promoting elastic and seamless access to research assets (data, services, computing) across the boundaries of institutions, disciplines and providers to favour collaboration-oriented research tasks. gCube's technology is primarily conceived to enable Hybrid Data Infrastructures facilitating the dynamic definition and operation of Virtual Research Environments. To this end, it offers a comprehensive set of data management commodities on various types of data and a rich array of "mediators" to interface well-established Infrastructures and Information Systems from various domains. Its effectiveness has been proved by operating the D4Science.org infrastructure and serving concrete, multidisciplinary, challenging, and large scale scenarios.Source: Future generation computer systems 95 (2019): 445–453. doi:10.1016/j.future.2018.10.035
DOI: 10.1016/j.future.2018.10.035
DOI: 10.5281/zenodo.3080894
DOI: 10.5281/zenodo.3080895
Project(s): AGINFRA PLUS
, BlueBRIDGE , ENVRI PLUS , EOSCpilot Metrics:
See at:
ZENODO | ZENODO | ISTI Repository | OpenAIRE | Future Generation Computer Systems | Future Generation Computer Systems | CNR ExploRA | www.sciencedirect.com
2019
Journal article
Open Access
Enacting open science by D4Science
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Sinibaldi F.
The open science movement is promising to revolutionise the way science is conducted with the goal to make it more fair, solid and democratic. This revolution is destined to remain just a wish if it is not supported by changes in culture and practices as well as in enabling technologies. This paper describes the D4Science offerings to enact open science-friendly Virtual Research Environments. In particular, the paper describes how complete solutions suitable for realising open science practices can be achieved by integrating a social networking collaborative environment with a shared workspace, an open data analytics platform, and a catalogue enabling to effectively find, access and reuse every research artefact.Source: Future generation computer systems (2019): 555–563. doi:10.1016/j.future.2019.05.063
DOI: 10.1016/j.future.2019.05.063
Project(s): AGINFRA PLUS, BlueBRIDGE , ENVRI PLUS , EOSCpilot
Metrics:
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Frosini L., Lelii L., Mangiacrapa F., Pagano P., Panichi G., Sinibaldi F.
The open science movement is promising to revolutionise the way science is conducted with the goal to make it more fair, solid and democratic. This revolution is destined to remain just a wish if it is not supported by changes in culture and practices as well as in enabling technologies. This paper describes the D4Science offerings to enact open science-friendly Virtual Research Environments. In particular, the paper describes how complete solutions suitable for realising open science practices can be achieved by integrating a social networking collaborative environment with a shared workspace, an open data analytics platform, and a catalogue enabling to effectively find, access and reuse every research artefact.Source: Future generation computer systems (2019): 555–563. doi:10.1016/j.future.2019.05.063
DOI: 10.1016/j.future.2019.05.063
Project(s): AGINFRA PLUS
, BlueBRIDGE , ENVRI PLUS , EOSCpilot Metrics:
See at:
ISTI Repository | Future Generation Computer Systems | CNR ExploRA
2019
Report
Restricted
DESIRA - Deliverable 5.1 - Virtual Research Environment: specification report
Assante M, Cirillo R., Dell'Amico A., Frosini L., Pagano P.
The DESIRA Virtual Research Environment specification consists of a hardware layer and a service layer. The former is made available by the D4Science Infrastructure 1 [1, 2] and it is organized as a dynamic pool of virtual machines, supporting computation and storage. The operations and management of those resources is performed via a set of enabling technologies selected to ensure availability and reliability of the infrastructure while e guaranteeing reduction of costs of ownership and a set of supporting technologies selected to ensure secure monitoring, alerting and provisioning. The service layer, illustrated in Figure 1, consists of three service frameworks, which can be summarized as a follows: o Enabling Framework: the enabling framework, framework , based on the gCube System [3], includes services required to support the operation of all services and the VREs supported by such services. As such it includes: a resource registry service, to which all e-infrastructure infrastructure resources (data sources, services, computational nodes, etc.) can be dynamically (de)registered and discovered by user and other services; Authentication and Authorization services, as well as Accounting Services, capable of both granting ing and tracking access and usage actions from users; and a VRE manager, capable of deploying in the collaborative framework VREs inclusive of a selected number of "applications", generally intended as sets of interacting services; o Storage Framework: the storage framework includes services for efficient, advanced, and on on-demand management of digital data, encoded as: files in a distributed file system, collection of metadata records, and time series in spatial databases; such services are used by all other services in the architecture, exception made for the enabling framework; o Collaborative framework : the collaborative framework includes all services deployed for the scientists and for each of them provides social networking services, user management services, shared workspace services. In addition, addition it comprises the part on the Web UI access to the Virtual Research Environment.Source: Project report, DESIRA, Deliverable D5.1, pp.1–19, 2019
Assante M, Cirillo R., Dell'Amico A., Frosini L., Pagano P.
The DESIRA Virtual Research Environment specification consists of a hardware layer and a service layer. The former is made available by the D4Science Infrastructure 1 [1, 2] and it is organized as a dynamic pool of virtual machines, supporting computation and storage. The operations and management of those resources is performed via a set of enabling technologies selected to ensure availability and reliability of the infrastructure while e guaranteeing reduction of costs of ownership and a set of supporting technologies selected to ensure secure monitoring, alerting and provisioning. The service layer, illustrated in Figure 1, consists of three service frameworks, which can be summarized as a follows: o Enabling Framework: the enabling framework, framework , based on the gCube System [3], includes services required to support the operation of all services and the VREs supported by such services. As such it includes: a resource registry service, to which all e-infrastructure infrastructure resources (data sources, services, computational nodes, etc.) can be dynamically (de)registered and discovered by user and other services; Authentication and Authorization services, as well as Accounting Services, capable of both granting ing and tracking access and usage actions from users; and a VRE manager, capable of deploying in the collaborative framework VREs inclusive of a selected number of "applications", generally intended as sets of interacting services; o Storage Framework: the storage framework includes services for efficient, advanced, and on on-demand management of digital data, encoded as: files in a distributed file system, collection of metadata records, and time series in spatial databases; such services are used by all other services in the architecture, exception made for the enabling framework; o Collaborative framework : the collaborative framework includes all services deployed for the scientists and for each of them provides social networking services, user management services, shared workspace services. In addition, addition it comprises the part on the Web UI access to the Virtual Research Environment.Source: Project report, DESIRA, Deliverable D5.1, pp.1–19, 2019
See at:
data.d4science.net | CNR ExploRA