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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 Report Open Access OPEN

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 via OpenAIRE

See at: data.d4science.net Open Access | 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 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

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


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 VREs operation activity: final report
Assante M., Candela L., Cirillo R., Dell'Amico A., Pagano P.
Virtual Research Environments and Virtual Laboratories are among the key products the BlueBRIDGE project is called to develop and to deliver to serve its target communities and application scenarios. The deployment and operation of a Virtual Research Environment is a task that involves the reuse of existing technologies as well as the development of new technologies aiming at offering new facilities. The development of the technology, both the generic as well as that which is oriented to serve the specific needs of a given community/target scenario, is captured by other deliverables. This report describes the activities performed to provide the BlueBRIDGE community with the set of Virtual Research Environments (VREs) and Virtual Laboratories (VLabs) hosted by the BlueBRIDGE portal during the entire duration of the project. A total of 66 VREs / VLabs have been deployed and operated, overall serving more than 3000 users across 32 countries and 124 different organizations. Such VREs / VLabs include "private" ones (66% circa), i.e. environments whose membership is by invitation only, "restricted" ones (15% circa), i.e. environments that users can request to join yet the requests have to be explicitly approved by the managers, and "open" ones (18% circa), i.e. environments that any user can request to join and no approval is needed. The 45% circa of the served users is exploiting "open" environments, the 34% circa is exploiting "private" environments, and the 19% circa is exploiting "restricted" environments. During the project, more than 980 requests for support, incident or bug have been resolved (441 requests for support and 546 requests for incidents and bugs).Source: Project report, BlueBRIDGE, Deliverable D4.5, 2018
Project(s): BlueBRIDGE via OpenAIRE

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


2018 Report Open Access OPEN

ENVRIplus - Interoperable data processing services for environmental RI projects: prototype
Candela L., Cirillo R., Coro G., Pagano P., Panichi G.
This deliverable documents the implementation of the data processing solution defined in D7.1 "Interoperable data processing for environmental RIs projects: system design". The actual deliverable consists of the software realising the envisaged solution and the instances of it made available to the ENVRI community in the large. The distinguishing features of the proposed solution are (a) to be suitable for serving the needs of scientists involved in ENVRI RIs, (b) to be open and extensible both with respect to the algorithms and methods it enables and the computing platforms it relies on to execute those algorithms and methods, (c) to be open-science-friendly, i.e. it is capable of incorporating every algorithm and method integrated into the data processing framework as well as any computation resulting from the exploitation of integrated algorithms into a "research object" catering for citation, reproducibility, repeatability and provenance. The proposed solution is part of a larger software system named gCube and has been provisioned to ENVRI RIs via several Virtual Research Environments operated by D4Science.Source: Project report, ENVRIplus, Deliverable D7.2, 2018
Project(s): ENVRI PLUS via OpenAIRE

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


2017 Software Unknown

SSTorage gCube service
Cirillo R.
A RESTful service providing functions for create, update, read a json object on MongoDB cluster.

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


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


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 VREs operation activity: interim report
Assante M., Candela L., Cirillo R., Dell'Amico A., Pagano P., Perciante C.
Virtual Research Environments and Virtual Laboratories are among the key products the BlueBRIDGE project is called to develop and to deliver to serve its target communities and application scenarios. The deployment and operation of a Virtual Research Environment is a task that involves the reuse of existing technologies as well as the development of new technologies aiming at offering new facilities. The development of the technology, both the generic as well as that which is oriented to serve the specific needs of a given community/target scenario, is captured by other deliverables. This report describes the activities performed to provide the BlueBRIDGE community with the set of Virtual Research Environments (VREs) and Virtual Laboratories (VLabs) hosted by the BlueBRIDGE portal from September 2015 to November 2016. A total of 38 VREs VLabs have been deployed and operated, overall serving more than 1500 users across 22 countries. This requested to deal with approximately 600 tickets (32 tickets for VRE creationupdate, 244 requests for support, 315 requests for incidents and bugs).Source: Project report, BlueBRIDGE, Deliverable D4.3, 2016
Project(s): BlueBRIDGE via OpenAIRE

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


2015 Software Unknown

gCube resource manager
Simi M., Cirillo R.
The Resource Manager is a SOA based service in charge of managing gCube Scope contexts. The Resource Manager 2.0, by coordinating five distinguished services (Deployer, Software Gateway, Resource Broker, gCube Hosting Node Manager, Web Hosting Node Manager), realizes the VRE dynamic deployment by, respectively, collecting service implementations, selecting target nodes for deployment within the infrastructure, and hosting resources implementations at selected nodes. The primary role assigned to this service is to collects and manage all the resources and service implementations related to a specific Virtual Organization.Project(s): IMARINE via OpenAIRE

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


2015 Software Unknown

gCube Whn manager
Cirillo R.
The Whn-Manager is a smartgears based service that operates in the context of gCube providing an interface for remotely managing a Web Hosting Node. In particular, this service is responsible for: the management and changes of the scope of the node and the locally deployed service instances according to the Scope Management rules; publishing in the Information System the gCube Resource representing the wHN.Project(s): IMARINE via OpenAIRE

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


2015 Software Unknown

Storage manager library for gCube
Cirillo R.
The storage manager library implements access and storage facilities, POSIX-Like API which supports the organisation and operations normally associated with local file systems whilst offering scalable and fault-tolerant remote storage.Project(s): D4SCIENCE-II via OpenAIRE

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


2014 Report Open Access OPEN

iMarine - iMarine Data Management Software
Coro G., Lelii L., Manzi A., Drakopoulos N., Marioli V., Cirillo R., Simeoni F., Antoniadis A., Brito F., Caumont H.
The iMarine Data Management Software comprises a number of components and subsystems offering facilities for accessing, transferring and harmonising a rich array of data typologies. This document describes the novelties within the iMarine Data Management Software from M12 (Oct.'12) to M27 (Jan.'14). It complements D9.2 [10] which describes iMarine Data Management Software up to M11 (Sept.'12). This deliverable is intended for documentation purposes only. The actual deliverable is represented by the software artifacts and their accompanying documentation.Source: Project report, iMarine, Deliverable D9.3, 2014
Project(s): IMARINE via OpenAIRE

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


2014 Report Open Access OPEN

IMARINE - iMarine Data e­-Infrastructure Operation Report
Candela L., Cirillo R., Manzi A., Pagano P.
The iMarine Data e-­Infrastructure is a living system whose development is mainly driven by requirements and feedback produced by the iMarine CoP. This deliverable is the third of the series of reports on the activities performed while operating such a system. The deliverable describes the state of the Data e-­Infrastructure in terms of nodes available, software deployed, quality of the service, and usage as of September 2014.Source: Project report, iMarine, Deliverable D5.4, 2014
Project(s): IMARINE via OpenAIRE

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