Pasquale Pagano

OpenDLib: A Digital Library Service System

OpenDLib is a software toolkit that can be used to create a digital library easily, according to the requirements of a given user community, by instantiating the software appropriately and then either loading or harvesting the content to be managed. OpenDLib consists of a federation of services that implement the digital library functionality making few assumptions about the nature of the documents to be stored and disseminated. If necessary, the system can be extended with other services to meet particular needs. The main focus of the paper is the openness and extendibility of the system. This feature has been obtained by applying a systematic approach to the design of the toolkit. A model of the system architecture has been defined in order to support this approach. The paper presents OpenDLib through this model.

DILIGENT: integrating digital library and Grid technologies for a new Earth observation research infrastructure

This paper introduces DILIGENT, a digital library infrastructure built by integrating digital library and Grid technologies and resources. This infrastructure allows different communities to dynamically build specialised digital libraries capable to support the entire e-Science knowledge production and consumption life-cycle by using shared computing, storage, content, and application resources. The paper presents some of the main software services that implement the DILIGENT system. Moreover, it exemplifies the provided features by presenting how the DILIGENT infrastructure is being exploited in supporting the activity of user communities working in the Earth Science Environmental sector.

A system for building expandable digital libraries

Expandability is one of the main requirements of future digital libraries. We introduce a digital library service system, OpenDLib, that has been designed to be highly expandable in terms of content, services and usage. We illustrate the mechanisms that enable expandability and discuss their impact on the development of the system architecture.

Species distribution modeling in the cloud

Species distribution modeling is a process aiming at computationally predicting the distribution of species in geographic areas on the basis of environmental parameters including climate data. Such a quantitative approach has a lot of potentialities in many areas that include setting up conservation priorities, testing biogeographic hypotheses, and assessing the impact of accelerated land use. To further promote the diffusion of such an approach, it is fundamental to develop a flexible, comprehensive, and robust environment capable of enabling practitioners and communities of practice to produce species distribution models more efficiently. A promising way to build such an environment is offered by modern infrastructures promoting the sharing of resources, including hardware, software, data, and services. This paper describes an approach to species distribution modeling based on a Hybrid Data Infrastructure that can offer a rich array of data and data management services by leveraging other infrastructures (including Cloud). It discusses the whole set of services needed to support the phases of such a complex process including access to occurrence records and environmental parameters and the processing of such information to predict the probability of a species’ occurrence in given areas.Copyright

Foundations of a Multidimensional Query Language for Digital Libraries

A query language for Digital Libraries is presented, which offers access to documents by structure and sophisticated usage of meta-data. The language is based on a mathematical model of digital library documents, centered around a multilevel representation of documents as versions, views and manifestations. The core of the model is the notion of document view, which is recursive, and captures the content and structure of a document. The metadata representation distinguishes between formats and specifications, so being able to accommodate different meta-data formats, even for the same document. A query is a logical formula, and its result are the digital library documents satisfying the user query.

The D-NET software toolkit

Purpose – The purpose of this paper is to present the architectural principles and the services of the D-NET software toolkit. D-NET is a framework where designers and developers find the tools for constructing and operating aggregative infrastructures (systems for aggregating data sources with heterogeneous data models and technologies) in a cost-effective way. Designers and developers can select from a variety of D-NET data management services, can configure them to handle data according to given data models, and can construct autonomic workflows to obtain personalized aggregative infrastructures. Design/methodology/approach – The paper provides a definition of aggregative infrastructures, sketching architecture, and components, as inspired by real-case examples. It then describes the limits of current solutions, which find their lacks in the realization and maintenance costs of such complex software. Finally, it proposes D-NET as an optimal solution for designers and developers willing to realize aggre...

Parallelizing the execution of native data mining algorithms for computational biology

Data mining is being increasingly used in biology. Biologists are adopting prototyping languages, like R and Matlab, to facilitate the application of data mining algorithms to their data. As a result, their scripts are becoming increasingly complex and also require frequent updates. Application to large datasets becomes impractical and the time‐to‐paper increases. Furthermore, even if there are various systems that can be used to efficiently process large datasets, for example, using Cloud and High Performance Computing, they usually require procedures to be translated into specific languages or to be adapted to a certain computing platform. Such modifications can speed up the processing, but translation is not automatic, especially in complex cases, and can require a large amount of programming effort and accurate validation. In this paper, we propose an approach to parallelize data mining procedures in the form of compiled software or R scripts developed by biology communities of practice. Our approach requires minimal alteration of the original code. In many cases, there is no need for code modification. Furthermore, it allows for fast updating when a new version is ready. We clarify the constraints and the benefits of our method and report a practical use case to demonstrate such benefits compared with a standard execution. Our approach relies on a distributed network of web services and ultimately exposes the algorithms as‐a‐Service, to be invoked by remote thin clients. Copyright

An Extensible Virtual Digital Libraries Generator

In this paper we describe the design and implementation of the VDL Generator, a tool to simplify and automatise the Digital Library development process. In particular, we discuss how our approach to the realisation of this tool simplifies the task of implementing, extending and modifying such a fundamental component. This tool models its issue as a generic search problem that can easily be adapted to different application scenarios. In particular, to guarantee its extensibility we carefully identify, isolate and organise the VDL Generator constituents, i.e. (i) the set of logical componentsthat can be used when designing a Digital Library, (ii) the set of physical componentsthat by implementing the logical components contribute to implement the Digital Library and (iii) the search strategyexploited to accomplish the generation task. Furthermore, we report on the experiences matured in implementing and exploiting such an innovative service in the context of the Diligent EU funded project and discuss future plans for its consolidation.

Developing a European Technical Reference Digital Library

The development of a European digital library for grey literature is described. The aim has been to provide a digital library for scientists working in the areas of information science and applied mathematics and also to build a test-bed for research activities. The service has been implemented as part of NCSTRL (the US Networked Computer Science Technical Reference Library) and developed, extending the Dienst system used by NCSTRL, to meet the requirements of the European scientific community. The additional functionality is described and the difficulties encountered when trying to extend an existing architecture, protocol and system are discussed.

Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure

EUBrazilOpenBio is a collaborative initiative addressing strategic barriers in biodiversity research by integrating open access data and user‐friendly tools widely available in Brazil and Europe. The project deploys the EU‐Brazil Hybrid Data Infrastructure that allows the sharing of hardware, software and data on‐demand. This infrastructure provides access to several integrated services and resources to seamlessly aggregate taxonomic, biodiversity and climate data, used by processing services implementing checklist cross‐mapping and ecological niche modelling. A Virtual Research Environment was created to provide users with a single entry point to processing and data resources. This article describes the architecture, demonstration use cases and some experimental results and validation. Copyright