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D4Science
D4Science is an organisation operating a Data Infrastructure offering a rich array of services by community-driven virtual research environments. In particular, it supports communities of practice willing to implement open science practices. The infrastructure follows the system of systems approach, where the constituent systems (Service providers) offer “resources” (namely services and by them data, computing, storage) assembled together to implement the overall set of D4Science services. In particular, D4Science aggregates “domain agnostic” service providers as well as community-specific ones to build a unifying space where the aggregated resources can be exploited via Virtual research Environments and their services. This organization is hosted by the Istituto di Scienza e Tecnologie dell'Informazione of National Research Council (Italy). At the earth of this infrastructure there is an Open Source Software named gCube system. Services D4Science offers a rich ar ...
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European Grid Infrastructure
European Grid Infrastructure (EGI) is a series of efforts to provide access to high-throughput computing resources across Europe using grid computing techniques. The EGI links centres in different European countries to support international research in many scientific disciplines. Following a series of research projects such as DataGrid and Enabling Grids for E-sciencE, the EGI Foundation was formed in 2010 to sustain the services of EGI. Purpose Science has become increasingly based on open collaboration between researchers across the world. It uses high-capacity computing to model complex systems and to process experimental results. In the early 21st century, grid computing became popular for scientific disciplines such as high-energy physics and bioinformatics to share and combine the power of computers and sophisticated, often unique, scientific instruments in a process known as e-Science. In addition to their scientific value, on 30 May 2008 The EU Competitiveness Council ...
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GCube System
gCube is an open source software system specifically designed and developed to enact the building and operation of a Data Infrastructure providing their users with a rich array of services suitable for supporting the co-creation of Virtual Research Environments and promoting the implementation of open science workflows and practices. It is at the heart of the D4Science Data Infrastructure. It is primarily organised in a number of web service called to offer functionality supporting the phases of knowledge production and sharing. In addition, it consists of a set of software libraries supporting service development, service-to-service integration, and service capabilities extension, and a set of portlets dedicated to realise user interface constituents facilitating the exploitation of one or more services. It is designed and conceived to enact system of systems. In fact, its gCube services rely on standards and mediators to interact with other services as well as are made avai ...
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Data Infrastructure
A data infrastructure is a digital infrastructure promoting data sharing and consumption. Similarly to other infrastructures, it is a structure needed for the operation of a society as well as the services and facilities necessary for an economy to function, the data economy in this case. Background There is an intense discussion at international level on e-infrastructures and data infrastructure serving scientific work. The European Strategy Forum on Research Infrastructures (ESFRI) presented the first European roadmap for large-scale Research Infrastructures. These are modeled as layered hardware and software systems which support sharing of a wide spectrum of resources, spanning from networks, storage, computing resources, and system-level middleware software, to structured information within collections, archives, and databases. The e-Infrastructure Reflection Group (e-IRG) has proposed a similar vision. In particular, it envisions e-Infrastructures where the principles o ...
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Istituto Di Scienza E Tecnologie Dell'Informazione
The "Alessandro Faedo" Istituto di Scienza e Tecnologie dell'Informazione (''Institute of Information Science and Technologies'') is an institute of the Italian National Research Council (CNR). The institute is located in the CNR research area in the Ghezzano Province of Pisa about 5 km from San Giuliano Terme. The institute was founded in 2002 as a merge of two previous CNR institutes: Istituto CNUCE and Istituto di Elaborazione dell’Informazione (IEI). The institute is named in honor of Alessandro Faedo, former President of CNR and former rector of the University of Pisa, for his important contributions to the development of Computer Science in Italy. The mission of the institute is ''producing scientific excellence and playing an active role in technology transfer'' in the field of Computer Science. In 2022 the research staff of the institute counts more than 120 researchers and a total staff (including PhD students and fellows) of around 230. Since 1 April 2019 the ISTI ...
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RStudio
RStudio is an integrated development environment for R, a programming language for statistical computing and graphics. It is available in two formats: RStudio Desktop is a regular desktop application while RStudio Server runs on a remote server and allows accessing RStudio using a web browser. Licensing model The RStudio integrated development environment (IDE) is available with the GNU Affero General Public License version 3. The AGPL v3 is an open source license that guarantees the freedom to share the code. RStudio Desktop and RStudio Server are both available in free and fee-based (commercial) editions. OS support depends on the format/edition of the IDE. Prepackaged distributions of RStudio Desktop are available for Windows, macOS, and Linux. RStudio Server and Server Pro run on Debian, Ubuntu, Red Hat Linux, CentOS, openSUSE and SLES. Overview and History The RStudio IDE is partly written in the C++ programming language and uses the Qt framework for its graphical ...
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Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ...
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KNIME
KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept. A graphical user interface and use of JDBC allows assembly of nodes blending different data sources, including preprocessing ( ETL: Extraction, Transformation, Loading), for modeling, data analysis and visualization without, or with only minimal, programming. Since 2006, KNIME has been used in pharmaceutical research, it also used in other areas such as CRM customer data analysis, business intelligence, text mining and financial data analysis. Recently attempts were made to use KNIME as robotic process automation (RPA) tool. KNIME's headquarters are based in Zurich, with additional offices in Konstanz, Berlin, and Austin (USA). History The Development of KNIME was started January 2004 by a team of software enginee ...
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Web Processing Service
The OGC Web Processing Service (WPS) Interface Standard provides rules for standardizing inputs and outputs (requests and responses) for invoking geospatial processing services, such as polygon overlay, as a web service. The WPS standard defines how a client can request the execution of a process, and how the output from the process is handled. It defines an interface that facilitates the publishing of geospatial processes and clients’ discovery of and binding to those processes. The data required by the WPS can be delivered across a network or they can be available at the server. WPS can describe any calculation (i.e. process) including all of its inputs and outputs, and trigger its execution as a web service. WPS supports simultaneous exposure of processes via HTTP GET, HTTP POST, and SOAP, thus allowing the client to choose the most appropriate interface mechanism. The specific processes served up by a WPS implementation are defined by the owner of that implementation. Althoug ...
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Reproducibility
Reproducibility, also known as replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or in a statistical analysis of a data set should be achieved again with a high degree of reliability when the study is replicated. There are different kinds of replication but typically replication studies involve different researchers using the same methodology. Only after one or several such successful replications should a result be recognized as scientific knowledge. With a narrower scope, ''reproducibility'' has been introduced in computational sciences: Any results should be documented by making all data and code available in such a way that the computations can be executed again with identical results. In recent decades, there has been a rising concern that many published scientific results fail the test of reproducibility, evoking a r ...
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Interactive Computing
In computer science, interactive computing refers to software which accepts input from the user as it runs. Interactive software includes commonly used programs, such as word processors or spreadsheet applications. By comparison, non-interactive programs operate without user intervention; examples of these include compilers and batch processing applications that are pre-programmed to run independently. Interactive computing focuses on real-time interaction ("dialog") between the computer and the operator, and the technologies that enable them. If the response of the computer system is complex enough, it is said that the system is conducting social interaction; some systems try to achieve this through the implementation of social interfaces. The nature of interactive computing as well as its impact on users, are studied extensively in the field of computer interaction. History of interactive computing systems Ivan Sutherland is considered the father of interactive computin ...
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Jupyter
Project Jupyter () is a project with goals to develop open-source software, open standards, and services for interactive computing across multiple programming languages. It was spun off from IPython in 2014 by Fernando Pérez and Brian Granger. Project Jupyter's name is a reference to the three core programming languages supported by Jupyter, which are Julia, Python and R. Its name and logo are an homage to Galileo's discovery of the moons of Jupiter, as documented in notebooks attributed to Galileo. Project Jupyter has developed and supported the interactive computing products Jupyter Notebook, JupyterHub, and JupyterLab. Jupyter is financially sponsored by NumFOCUS. History The first version of Notebooks for IPython was released in 2011 by a team including Fernando Pérez, Brian Granger, and Min Ragan-Kelley. In 2014, Pérez announced a spin-off project from IPython called Project Jupyter. IPython continues to exist as a Python shell and a kernel for Jupyter, while the ...
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R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ...
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