2023 Report Open Access

Implementation of a drug discovery pipeline on the D4Science platform
Orro A., D'Ursi P., Fossa P., Candela L., Panichi G.
This report documents the implementation of drug discovery pipeline in the D4Science platform realised in the context of the EOSC-Pillar project. In particular, it documents the pipeline and its constituents. Moreover, it describes how this pipeline has been integrated into the D4Science platform and exploited to create a dedicated Virtual Research Environment facilitating its exploitation and promoting a collaborative oriented approach for screening activities.Source: ISTI Technical Report, ISTI-2023-TR/001, 2023
DOI: 10.32079/isti-tr-2023/001
Project(s): EOSC-Pillar
Metrics:

See at: ISTI Repository | CNR ExploRA

2023 Journal article Open Access

D4SCIENCE: a unique infrastructure delivering virtual research environments as a service
Candela L., Castelli D., Pagano P.
Nowadays, research challenges - often based on the collaborative analysis of a large amount of data - require suitable infrastructures and user-facing solutions promoting multidisciplinary collaboration and appropriate communication and sharing of data, processes, and outcomes. The D4Science infrastructure and its virtual research environments proved to be a viable and effective solution for many communities of practice and use cases.Source: ERCIM news 133 (2023): 6–7.
Project(s): Blue Cloud , SoBigData-PlusPlus

See at: ercim-news.ercim.eu | ISTI Repository | CNR ExploRA

2023 Report Open Access

See at: ISTI Repository | CNR ExploRA

2023 Report Open Access

Janet: a prototype of a conversational agent for a virtual research environment
Ibrahim A. S. T., Candela L.
Conversational agents have been undergoing a lot of development where they have reached their best nowadays thanks to the large language models that have been developed over the past years. Thanks to this, the capabilities of such agents have become more diverse and they are now able to perform a wide range of tasks which can be harnessed to reduce or even replace the human effort in performing those tasks. Therefore, in an effort to equip scientific communities with such a powerful tool, we developed a prototype conversational agent, Janet, and deployed it into one virtual research environment (VRE) with the aim of supporting the scientists in exploiting the knowledge contained within these environments. Janet is still in the preliminary phase where there is a need for extensive testing and improvement; however, this report shows the main aspects of Janet including the architecture, implementation and deployment.Source: ISTI Technical Report, ISTI-2023-TR/006, 2023
DOI: 10.32079/isti-tr-2023/006
Project(s): Blue Cloud
Metrics:

See at: ISTI Repository | CNR ExploRA

2023 Journal article Open Access

The D4Science experience on virtual research environment development
Candela L., Castelli D., Pagano P.
Today, complex research challenges, often based on the analysis of a large amount of data, require multidisciplinary collaboration and appropriate communication and sharing of data, processes and outcomes. Technologies and large-scale infrastructures provide stakeholders with computing capacity and data services to perform unprecedented levels of data-driven scientific activities. This opens the way to science gateways and virtual research environments supporting researchers in scientific and educational activities. This article describes our extensive experience with the Virtual Research Environments (VRE) operated by the D4Science infrastructure. It presents how this infrastructure supports their development, their basic functionalities and how they are easily customised to serve the needs of specific user communities. It also describes how they are used in real contexts. The article concludes by reporting how VREs are now progressively used as valuable instruments to support open science and how this role might become more relevant in the future.Source: Computing in science & engineering (Online) 25 (2023). doi:10.1109/MCSE.2023.3290433
DOI: 10.1109/mcse.2023.3290433
Project(s): Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus
Metrics:

See at: ISTI Repository | ieeexplore.ieee.org | CNR ExploRA

2023 Report Open Access

Conversational agents for virtual research environments: a survey of the literature
Ibrahim A. S. T., Candela L.
Conversational artificial intelligence is becoming a rather hot topic in the field of artificial intelligence especially after the release of ChatGPT by OpenAI. That is why it is useful to conduct a survey of the literature regarding conversational agents in order to have an idea about the techniques used to develop such systems. Therefore, the aim of this report is to aggregate and summarize the previous research efforts in order to provide insight that would aid future researchers. In addition, the survey was conducted within the context of developing Janet, a conversational agent for virtual research environments; thus, it can be used as a starting point for similar projects.Source: ISTI Technical Report, ISTI-2023-TR/007, 2023
DOI: 10.32079/isti-tr-2023/007
Project(s): Blue Cloud
Metrics:

See at: ISTI Repository | CNR ExploRA

2023 Journal article Open Access

ARIADNE Plus e il D4GNA-Dataset per il Geoportale Nazionale per l'Archeologia
Acconcia V., Boi V., Candela L., Falcone A., Mangiacrapa F., Massara F., Pagano P., Sinibaldi F.
L'articolo racconta l'esperienza del D4GNA - Dataset per il Geoportale Nazionale dell'Archeologia nato nell'ambito del progetto ARIADNEplus (Advanced Research Infrastructure for Archaeological Dataset Networking in Europe - plus), conclusosi lo scorso 31 dicembre. Il contributo parte dal contesto più ampio del progetto europeo per addentrarsi nel mondo dei dati archeologici italiani; la soluzione tecnologica, la standardizzazione, la dematerializzazione e la condivisione in rete dei dati sono i temi toccati in questo percorso che ci illustra il procedere verso un obiettivo virtuoso: il Geoportale Nazionale per l'Archeologia (GNA). Il GNA, realizzato dall'Istituto Centrale per l'Archeologia (ICA) e che sarà in rete dal 10 luglio 2023, è il punto di accesso nazionale per accogliere e consultare gli interventi archeologici svolti sotto la direzione scientifica del Ministero della Cultura (MiC), le indagini archeologiche condotte da università e altri enti di ricerca, nonché altre banche dati territoriali.Source: Digitalia (Online) 1 (2023): 129–140. doi:10.36181/digitalia-00064
DOI: 10.36181/digitalia-00064
Project(s): ARIADNEplus
Metrics:

See at: digitalia.cultura.gov.it | ISTI Repository | CNR ExploRA

The gCube geoportal platform
Candela L., Cirillo R., Mangiacrapa F., Pagano P., Sinibaldi F., Vannini G. L.
The gCube Geoportal platform is a component of the gCube open source software system conceived to support the creation and publication of georeferenced research objects, i.e. multi-part and multimedia research objects characterised by geospatial and temporal features. The Geoportal platform enables user communities to fully customise the data model characterising their instance by defining the structure, the content and the workflow of the potential research objects to be managed. `this report carefully describes the technology and documents how it was exploited to serve the development of a national catalogue for archaeological artifacts.Source: ISTI Technical Report, ISTI-2023-TR/012, 2023
DOI: 10.32079/isti-tr-2023/012
Project(s): ARIADNEplus , Blue Cloud
Metrics:

See at: CNR ExploRA

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.Source: ISTI Annual Reports, 2023
DOI: 10.32079/isti-ar-2023/002
Project(s): Blue Cloud , EOSC Future , TAILOR
Metrics:

See at: CNR ExploRA

2023 Report 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).Source: ISTI Project report, DESIRA, D5.3, 2023
Project(s): DESIRA

See at: ISTI Repository | CNR ExploRA

2023 Report 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).Source: ISTI Project report, SoBigData-PlusPlus, D9.2, 2023
Project(s): SoBigData-PlusPlus

See at: ISTI Repository | CNR ExploRA

2023 Report Open Access

See at: ISTI Repository | CNR ExploRA

Recommender systems for science: a basic taxonomy
Arezoumandan M., Ghannadrad A., Candela L., Castelli D.
This dataset is accompanying the "Recommender system for science: A basic taxonomy" paper published at IRCDL 2022 conference. This study had a Systematic Mapping Approach on the Recommender system for science. In particular, the study aims at responding to four questions on recommender systems in science cases: users and their interests representation, item typologies and their representation, recommendation algorithms, and evaluation, and then providing a taxonomy. This dataset contains 209 papers of interest that have been published between 2015 and 2022. The dataset has 11 columns which organised as follows: Column Title: This column contains the title of the papers. Column DOI: This column contains the DOI of the papers. Column Publication_year: This column contains the year that the paper is published. Column DB: This column contains the repository that the paper is retrieved. Column Keywords: This column contains the keywords provided for the paper. Column Content_type: This column contains the paper type which can be: Article, Conference or Review. Column Citing_paper_count: This column contains the citation number of the paper. Column Recommended_artefact: This column contains the scientific product that is recommended to users which can be paper, workflow, collaborator, dataset or others. Column User_type: This column contains the type of user who receives the recommendation, which can be an Individual user or a Group of users. Column Algorithm: This column contains the recommendation algorithm that the paper proposed, which can be: HB (Hybrid-based), CB (Content-based), CFB (Collaborative-filtering-based), or GB (Graph-based). Column Evaluation_method: This column contains the method of the algorithm evaluation which can be OFFLINE, ONLINE, BOTH, or NO_EVALUATION.DOI: 10.5281/zenodo.6006905
Project(s): Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus
Metrics:

See at: CNR ExploRA

2022 Contribution to conference Open Access

Recommender systems for science: a basic taxonomy
Arezoumandan M., Ghannadrad A., Candela L., Castelli D.
The ever-growing availability of research artefacts of potential interest for users calls for helpers to assist their discovery. Artefacts of interest vary for the typology, e.g., papers, datasets, software. User interests are multifaceted and evolving. This paper analyses and classifies studies on recommender systems exploited to suggest research artefacts to researchers regarding the type of algorithm, users and their representations, item typologies and their representation, and evaluation methods used to assess the effectiveness of the recommendations. This study found that most of the current scientific artefacts recommender system focused only on recommending paper to individual researchers, just a few papers focused on dataset recommendation and software recommender system is unprecedented.Source: IRCDL 2022 - 18th Italian Research Conference on Digital Libraries, Padova, Italy, 24-25/02/2022
Project(s): Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus

See at: ISTI Repository | CNR ExploRA

A taxonomy of tools and approaches for FAIRification
Mangione D., Candela L., Castelli D.
Datasets accompanying the study "A Taxonomy of Tools and Approaches for FAIRification" on the tools and approaches emerging from stakeholders' experiences adopting the FAIR principles in practice.DOI: 10.5281/zenodo.6037508
Project(s): Blue Cloud , EOSC-Pillar , DESIRA , SoBigData-PlusPlus
Metrics:

See at: CNR ExploRA

2022 Contribution to conference Open Access

A taxonomy of tools and approaches for FAIRification
Mangione D., Candela L., Castelli D.
The FAIR principles have drawn a lot of attention since their publication in 2016. A broad range of stakeholders is confronting the implementation of these guiding principles in diverse contexts.This paper identifies and discusses the tools and approaches emerging from stakeholders' experiences adopting the FAIR principles in practice. In particular, 225 open access grey literature papers (namely, deliverables, milestones and data management plans) on FAIRification have been scrutinised to infer tools and approaches in use. The wealth of emerging tools (477) has been carefully analysed and organised into a comprehensive map highlighting the significant classes of instruments supporting FAIRification. A critical discussion on this collection of tools and approaches and the FAIRification completes the paper.Source: IRCDL 2022 - 18th Italian Research Conference on Digital Libraries, Padova, Italy, 24-25/02/2022
Project(s): Blue Cloud , EOSC-Pillar , DESIRA , SoBigData-PlusPlus

See at: ISTI Repository | CNR ExploRA

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:

See at: ISTI Repository | onlinelibrary.wiley.com | CNR ExploRA

2022 Conference article Open Access

Recommender systems for science: a basic taxonomy
Ghannadrad A., Arezoumandan M., Candela L., Castelli D.
The ever-growing availability of research artefacts of potential interest for users calls for helpers to assist their discovery. Artefacts of interest vary for the typology, e.g. papers, datasets, software. User interests are multifaceted and evolving. This paper analyses and classifies studies on recommender systems exploited to suggest research artefacts to researchers regarding the type of algorithm, users and their representations, item typologies and their representation, and evaluation methods used to assess the effectiveness of the recommendations. This study found that most of the current scientific artefacts recommender system focused only on recommending paper to individual researchers, just a few papers focused on dataset recommendation and software recommender system is unprecedented.Source: IRCDL 2022 - 18th Italian Research Conference on Digital Libraries, Padua, Italy, 24-25/02/2022
Project(s): Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus

See at: ceur-ws.org | ISTI Repository | CNR ExploRA

2022 Conference article Open Access

A taxonomy of tools and approaches for FAIRification
Mangione D., Candela L., Castelli D.
The FAIR principles have drawn a lot of attention since their publication in 2016. A broad range of stakeholders is confronting the implementation of these guiding principles in diverse contexts. This paper identifies and discusses the tools and approaches emerging from stakeholders' experiences adopting the FAIR principles in practice. In particular, 225 open access grey literature papers (namely, deliverables, milestones and data management plans) on FAIRification have been scrutinised to infer tools and approaches in use. The wealth of emerging tools (477) has been carefully analysed and organised into a comprehensive map highlighting the significant classes of instruments supporting FAIRification. A critical discussion on this collection of tools and approaches and the FAIRification completes the paper.Source: IRCDL 2022 - 18th Italian Research Conference on Digital Libraries, Padua, Italy, 24-25/02/2022
Project(s): Blue Cloud , EOSC-Pillar , DESIRA , SoBigData-PlusPlus

See at: ceur-ws.org | ISTI Repository | CNR ExploRA

Virtual research environments ethnography: a preliminary study
Arezoumandan M., Candela L., Castelli D., Ghannadrad A., Mangione D., Pagano P.
This dataset is accompanying the paper "Virtual Research Environments Ethnography: a Preliminary Study" paper published at 14th International Workshop on Science Gateways 15th-17th June 2022, Trento, Italy. This is a systematic mapping study on the literature about Science gateways, Virtual Research Environments, and Virtual Laboratories.DOI: 10.5281/zenodo.6481183
Project(s): Blue Cloud , EOSC-Pillar , DESIRA , SoBigData-PlusPlus
Metrics:

See at: CNR ExploRA