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2021 Report Open Access OPEN

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 via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2021 Conference article Open Access OPEN

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 via OpenAIRE

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


2020 Journal article Open Access OPEN

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 via OpenAIRE

See at: ISTI Repository Open Access | Concurrency and Computation Practice and Experience Restricted | Concurrency and Computation Practice and Experience Restricted | Concurrency and Computation Practice and Experience Restricted | Concurrency and Computation Practice and Experience Restricted | CNR ExploRA Restricted | Concurrency and Computation Practice and Experience Restricted


2020 Report Open Access OPEN

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 via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2019 Journal article Open Access OPEN

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
Project(s): AGINFRA PLUS via OpenAIRE, BlueBRIDGE via OpenAIRE, ENVRI PLUS via OpenAIRE, EOSCpilot via OpenAIRE

See at: ISTI Repository Open Access | Future Generation Computer Systems Open Access | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | CNR ExploRA Restricted | Future Generation Computer Systems Restricted | www.sciencedirect.com Restricted


2019 Journal article Open Access OPEN

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 via OpenAIRE, BlueBRIDGE via OpenAIRE, ENVRI PLUS via OpenAIRE, EOSCpilot via OpenAIRE

See at: ISTI Repository Open Access | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | Future Generation Computer Systems Restricted | CNR ExploRA Restricted | Future Generation Computer Systems Restricted


2019 Software Unknown

gfeed service
Sinibaldi F.
gFeed is an extendable gCube service which manages both Data Retrieval from multiple sources and Data Transformation and publication towards multiple destinations.Project(s): AGINFRA PLUS via OpenAIRE

See at: CNR ExploRA | wiki.gcube-system.org


2019 Software Unknown

PerformFish service
Sinibaldi F.
PerformFish Service is a REST Service aimed to anonymize and manage data for the PerformFish projectProject(s): PerformFISH via OpenAIRE

See at: maven.research-infrastructures.eu | CNR ExploRA


2019 Report Restricted

PARTHENOS - Deliverable 6.6 - PARTHENOS Cloud Infrastructure
Pagano P., Assante M., Frosini L., Manghi P., Bardi A., Sinibaldi F., Cirillo R., Panichi G.
"D6.6 PARTHENOS cloud infrastructure" is the revised and final version of "D6.1 PARTHENOS cloud infrastructure". This deliverable reports the PARTHENOS e-infrastructure architecture: the hardware and the services. Hardware is organized as a dynamic cloud of virtual machines, supporting computation and storage, while the services are organized into e-infrastructure middleware, storage, and end user services.Source: Project report, PARTHENOS, Deliverable D6.6, pp.1–63, 2019
Project(s): PARTHENOS via OpenAIRE

See at: data.d4science.net Restricted | CNR ExploRA Restricted


2018 Report Open Access OPEN

BlueBRIDGE - BlueBRIDGE VRE commons facilities: revised version
Assante M., Candela L., Coro G., Koltsida P., Laskaris N., Marketakis Y., Sinibaldi F., Pagano P.
Deliverable D9.2 - "BlueBRIDGE VRE Commons Facilities: Revised Version" is the revised version of the D9.1 deliverable, intended to report the release of the BlueBRIDGE facilities for Data Access, Data Discovery, Data Storage, Data Analytics and Data Publishing. It is conceived to include the latest developments and releases that took place between the 2 versions of the reports. The deliverable is of type "Other" and the following document is intended to provide its readers with an easy-to-use description of the actual components, services and systems contributing to form the BlueBRIDGE VRE Commons Facilities. This document is structured as follows: a description for each facility is available, in conjunction with links to the project's wiki, providing more detailed descriptions and additional information for each component. This revised version of the document aims at providing a complete picture of the available facilities for Accessing, Discovering, Storing Data, Analysing and Publishing Data developed through the project's lifetime. The deliverable is divided in two main sections. The first one follows the structure of Work Package 9; specifically, it documents the various releases and versions of the facilities available for Accessing, Discovering and Storing Data (T9.1), for Analysing Data (T9.2) and for Publishing Data (T9.3). The second section comprises facilities for managing and using VREs that span across all the three WP9 tasks. Specifically, it includes dedicated parts documenting the various releases and versions of services for defining, creating and deploying VREs (VRE Management facilities) together with a set of applications allowing to use the VRE through a thin client (VRE Enabling facilities). The deliverable provides, for each facility, a description, the documentation for developers and system administrators, how-to guides and usage instructions for different use cases and links to open source code and binaries. Further details and the complete documentation for the facilities are available on the gCube wiki at https://wiki.gcube-system.org/gcube/About_gCube. The intended readers of this deliverable are (a) the community in the large willing to be informed on the solutions BlueBRIDGE offers for VRE management, Data Access, Discovery, Storage, Analytics and Publishing, and (b) the gCube developer community to know how to integrate, use and build on top of the facilities described by the document.Source: Project report, BlueBRIDGE, Deliverable D9.2, 2018
Project(s): BlueBRIDGE via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2018 Report Open Access OPEN

D10.2 BlueBRIDGE Resources Federation Facilities : Revised Version
Candela L., Coro G., Fabriani P., Frosini L., Galante N. A., Giammatteo G., Pavia D., Kakaletris G., Lelii L., Simi M., Sinibaldi F., Koltsida P.
Deliverable D10.2 - "BlueBRIDGE Resources Federation Facilities: Revised Version" reports the release of the BlueBRIDGE facilities for integration of resources from external infrastructures and management of integrated resources. It is structured as follows: a description for each facility is available on this document in conjunction witha list of the main features, information about the design and architecture of it, a number of use cases and finally how it can be deployed. In case more information is needed or a more detailed documentation is available, URLs to the project 's wiki are provided. The set of the available facilities are split in three main categories: (a) facilities for integrating computing infrastructure resources, aiming on exploiting the computational power offered by external infrastructures in order to execute CPU intensive jobs, (b) facilities for integrating data infrastructure resources, where a number of components have been developed in order to integrate data from different data infrastructures to in the Virtual Research Environments (VREs), including biodiversity, geospatial and generic OAI-PMH repositories and (c) facilities for federated resources management, for effectively and efficiently managing the federated resources made available thanks to bridges developed in the previous categories. The sections that follow provide the description and the details for each distinct facility, aiming on offering a complete guide to the intended readers. The intended readers of this deliverable are (a) the community in the large willing to be informed on the solutions BlueBRIDGE offers for federated resources management, (b) the gCube developer community to know how to integrate, use and build on top of the facilities described by the document, and (c) the gCube administrators to know how to setup, configure and manage the integration of a gCube infrastructure with external resources.Source: Project report, BlueBRIDGE, Deliverable D10.2, pp.1–54, 2018
Project(s): BlueBRIDGE via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2017 Report Open Access OPEN

AGINFRA PLUS - Open Science Data Analytics Technologies D3.1
Candela L., Cirillo R., Coro G., Lelii L., Pagano P., Panichi G., Scarponi P., Sinibaldi F.
Deliverable D3.1 "Open Science Data Analytics Technologies" is a deliverable of type Demonstrator meaning that it manifests in artefacts (software releases) other than reports. In particular, the deliverable is about the software realising the Data Analytics & Processing Layer of the AGINFRA+. This software is part of a large software system named gCube (www.gcube-system.org). The gCube system offers a large array of services supporting the entire lifecycle underlying a research activity (data management and collation, analytics, collaboration, sharing) and the possibility to combine these services in Virtual Research Environments1. In the context of AGINFRA PLUS the following gCube components have been primarily exploited, consolidated and enhanced to serve the analytics needs arising in the context of the project use cases. DataMiner, i.e. a service enacting its users to perform data analytics tasks by relying on an array of analytics methods and a distributed and heterogeneous computing infrastructure. This service is available by a web-based GUI as well as via a web-based API based on the OGC WPS standard. SAI (Statistical Algorithm Importer), i.e. a service enacting its users to make available their own analytics methods via the DataMiner service. In addition to that, the entire analytics solution made available for AGINFRA PLUS cases counts on (i) a shared workspace realising a cloud-based file manager for managing content of interest and sharing this content with co-workers, (ii) a social networking area enabling users to post messages and have discussions, (iii) a flexible catalogue enabling to publish and discover items of interest including "research objects" resulting from an analytics task. This technology is deployed in its latest version in every Virtual Research Environment supporting AGINFRA PLUS cases2. The major enhancements to the technology pertaining to AGINFRA PLUS have been included in three gCube major releases3 4.7 (October 2017), 4.8 (November 2017), and 4.9 (under production).In particular, with these releases a new"black-box" oriented approach (https://wiki.gcubesystem. org/gcube/Statistical_Algorithms_Importer:_Java_Project#Black_Box_Integration)has been envisaged and implemented to enact analytics method owners and developers to easily integrate theirsolutions into the DataMinerservice. Among the supported black-box typologies there is that for KNIME workflows, i.e. analytics methods implemented by a KNIME workflow. KNIME is among the key technologies supporting the Food Safety Risk Assessment cases. In order to enact the execution of KNIME-based black-boxes, the distributed computing part of the data analytics platform has been extended to integrate the KNIME execution engine. Other cases are counting on the same mechanism to integrate entire applications (WOFOST4) as well as Python-based methods.Source: Project report, AGINFRA PLUS, Deliverable D3.1, pp.1–4, 2017
Project(s): AGINFRA PLUS via OpenAIRE

See at: CNR ExploRA Open Access | support.d4science.org Open Access


2017 Software Unknown

SDI Suite
Sinibaldi F.
SDI Suite is a collection of software aimed to let applications interact with the Spatial Data Infrastructure operated in D4ScienceProject(s): BlueBRIDGE via OpenAIRE

See at: CNR ExploRA | wiki.gcube-system.org


2017 Software Unknown

Gcube 4.8.0 - Ws-Thredds V. 0.0.2
Sinibaldi F.
WS-Thredds is a library dedicated to two-way synchronization of a gCube WS Folder with a THREDDS catalogue, by exploiting Data Transfer Service and SDI Service capabilities.Project(s): BlueBRIDGE via OpenAIRE

See at: CNR ExploRA


2016 Report Open Access OPEN

BlueBRIDGE - D9.1 BlueBRIDGE VRE Commons Facilities
Assante M., Candela L., Cirillo R., Coro G., Koltsida P., Marioli V., Perciante C., Sinibaldi F.
Deliverable D9.1 - "BlueBRIDGE VRE Commons Facilities" reports the release of the BlueBRIDGE facilities for Data Access, Data Discovery, Data Storage, Data Analytics and Data Publishing. Those facilities are implemented through web services, libraries, and mediators over technologies that are offered as services operated and made accessible through VREs This deliverable is of type "Other" and consists of a set of wiki pages hosted by the BlueBRIDGE project wiki [1] plus a set of documentation pages for single facilities hosted by the gCube wiki [2].Source: Project report, BlueBRIDGE, Deliverable D9.1, 2016
Project(s): BlueBRIDGE via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Restricted


2016 Report Open Access OPEN

BlueBRIDGE - BlueBRIDGE resources federation facilities
Candela L., Coro G., Frosini L., Galante N. A., Giammatteo G., Kakaletris G., Lelii L., Marioli V., Sinibaldi F.
Deliverable D10.1 - "BlueBRIDGE Resources Federation Facilities" reports the release of the BlueBRIDGE facilities for integration of resources from external infrastructures and management of integrated resources. The deliverable covers the first nine months of the BlueBRIDGE project. An update to this deliverable is expected at project month M28 with Deliverable D10.2.Source: Project report, BlueBRIDGE, Deliverable D10.1, 2016
Project(s): BlueBRIDGE via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2016 Report Open Access OPEN

EGI-Engage - Deployment of a gCube release with federated cloud support
Fabriani P., Viljoen M., Giammatteo G., Sinibaldi F., Pagano P., Galante N. A.
This document reports on the integration of Federated Cloud resources in the D4Science platform, built on top of the gCube framework. The document introduces the D4Science platform, how it is currently exploited by scientific communities and motivates the need for the integration. The most relevant usage scenarios are analysed and corresponding requirements are identified. The extension to the gCube framework is defined in terms of overall architecture and description of single components. A number of enhancements have been selected for future evaluation and realization.Source: Project report, EGI-Engage, Deliverable D4.5, 2016
Project(s): EGI-Engage via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2016 Report Open Access OPEN

PARTHENOS - PARTHENOS Cloud Infrastructure
Pagano P., Candela L., Assante M., Frosini L., Manghi P., Bardi A., Sinibaldi F.
This report describes the PARTHENOS e-infrastructure architecture: the hardware and the services. Hardware is organized as a dynamic cloud of virtual machines, supporting computation and storage, while the services are organized into e-infrastructure middleware, storage, and end user services.Source: Project report, PARTHENOS, Deliverable D6.1, 2016
Project(s): PARTHENOS via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access


2016 Software Unknown

gCube Data Transfer Suite
Sinibaldi F.
gCube Data Transfer Suite is a collection of software libraries and service aimed to provide gCube Applications with a common layer for efficient and transparent data transfer towards gCube SmartGear nodes. It's designed as a client-server architecture exploiting plugin design pattern.Project(s): BlueBRIDGE via OpenAIRE

See at: CNR ExploRA | wiki.gcube-system.org


2014 Report Open Access OPEN

ENVRI - Integration, harmonisation and publication software components - version 2
Candela L., Coro G., Italiano A., Mangiacrapa F., Pagano P., Sinibaldi F.
The ENVRI Integration, Harmonisation and Publication software comprises a number of components, services and subsystems offering facilities enabling the integration and harmonization of data. The actual deliverable is thus the software realising such facilities. This document briefly describes the software components realising version 2 of these facilities and offers a series of links to the software itself and its accompanying documentationSource: Project report, ENVRI, Deliverable D4.5, 2014
Project(s): ENVRI via OpenAIRE

See at: ISTI Repository Open Access | CNR ExploRA Open Access